Nucleic acid hairpin probes and uses thereof

ABSTRACT

This invention relates generally to nucleic acid hybridization analysis. More specifically, an oligonucleotide probe for hybridization analysis is provided, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with. Arrays comprising the hairpin probes immobilized on a solid support and methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided. Methods for transcribing and/or amplifying a probe DNA sequence using a hairpin probe are further provided.

[0001] This application is a continuation-in-part of U.S. patent application Ser. No. 09/616,761, filed Jul. 14, 2000, now pending. The disclosure of the above-referenced application is incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

[0002] This invention relates generally to nucleic acid hybridization analysis. More specifically, an oligonucleotide probe for hybridization analysis is provided, that comprises a nucleotide sequence which, under suitable conditions, is capable of forming a hairpin structure. The probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains more at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with. Arrays comprising the hairpin probes immobilized on a solid support for hybridization analysis and methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided. Methods for transcribing and/or amplifying a probe DNA sequence using a hairpin probe are further provided.

BACKGROUND OF THE INVENTION

[0003] Nucleic acid hybridization, in the forty years since its discovery, has become a powerful tool with implications for biology, medicine and industry. Hybridization assays are based on the very specific base pairing that is found in hybrids of DNA and RNA. Base sequences of analytical interest appearing along a strand of nucleic acid can be detected very specifically and sensitively by observing the formation of hybrids in the presence of a probe nucleic acid known to comprise a base sequence that is complementary with the sequence of interest. Nucleic acid hybridization has been used for a wide variety of purposes including, for example, identification of specific clones from cDNA and genomic libraries, detecting single base pair polymorphisms in DNA, generating mutations by oligonucleotide mutagenesis, amplifying nucleic acids from single cells or viruses, or detecting microbial infections.

[0004] Recent advances in nucleic acid hybridization methods have greatly expanded the scope and extent of its potential applications. Of great interest are approaches to miniaturize hybridization reactions by preparing “microarray biochips” (or “DNA chips”) containing large numbers of oligonucleotide probes prepared, for example, through VLSIPS™ technology (See U.S. Pat. Nos. 5,143,854 or 5,561,071). These approaches offer great promise for a wide variety of applications. Microarray biochips are useful for sequencing nucleic acid by hybridization (see, for example, U.S. Pat. No. 5,741,644), for diagnosis of human immunodeficiency virus (see, for example, U.S. Pat. No. 5,861,242) and for screening potential DNA binding drugs (see, for example, U.S. Pat. No. 5,556,752).

[0005] When using nucleic acid microarrays, there are two general approaches for detecting hybridization to a nucleic acid. Detection can be accomplished if the target nucleic acid is labeled (“direct labeling approach”). Alternatively, detection can be accomplished by a second probe that is detectably labeled and which can hybridize to the nucleic acid of the sample, which is hybridized to the first probe immobilized on the array (“indirect” labeling approach).

[0006] Bagwell, U.S. Pat. No. 5,607,834 discloses a fluorescent probe for binding to a polynucleotide target and methods using such fluorescent probes that comprises: an oligonucleotide having a segment complementary to the polynucleotide target, the oligonucleotide forming two imperfect hairpins both of which together include the segment except for one nucleotide; and one donor fluorophore and one acceptor fluorophore covalently attached to the oligonucleotide so that only when the imperfect hairpins are formed, the donor fluorophore and the acceptor fluorophore are in close proximity to allow resonance energy transfer therebetween. The fluorescent probes disclosed in Bagwell must contain “imperfect hairpins,” i.e., containing mismatches in the double-stranded stem segment. In addition, Bagwell does not disclose or teach any immobilized arrays of oligonucleotide probes.

[0007] Nazarenko et al., U.S. Pat. No. 5,866,336 disclose an oligonucleotide containing a hairpin structure for use as a primer in detecting a target nucleotide sequence. Similar probes are described in Mergny et al., Nucleic Acids Res., 22:920-928 (1994). Blok and Kramer, Molecular and Cellular Probes, 11:187-194 (1997) describe an amplification RNA probe containing a molecular switch, i.e., a plurality of hairpin structures. Fujiwara and Oishi, Nucleic Acids Res., 26:5728-5733 (1998) describe a method of covalent attachment of probe DNA to double-stranded target DNA where an imperfect hairpin was used to hybridize to a target DNA. Sriprakash and Hartas, Gene Anal. Techn., 6:29-32 (1989) describe a method of generating radioisotope labeled probe with hairpin nucleic acid structure. One common feature of the hairpin structure-containing probes described in the above references is that the nucleotide sequence complementary to a target nucleotide sequence always resides in the single-stranded, not double-stranded, segment of the hairpin structure.

[0008] The direct labeling approach can be problematic because nucleic acid labeling methods may fail to label different nucleic acids in a mixture equally. In addition, direct labeling may introduce mutations or other chemical modifications of the sample nucleic acid that prohibit or reduce hybridization.

[0009] Detection of hybridization in a microarray biochip by indirect labeling also can be problematic because background hybridization between the second probe may hybridize to the first probe immobilized on the microarray, giving rise to a high false-positive assay background. If the microarray utilizes only a single probe or very limited set of probes, the background may be reduced in the indirect labeling format by designing the specific second probe such that it does not hybridize to the immobilized probes on the array. However, when the microarray contains a wide variety of probe sequences for simultaneously detecting a variety of different nucleic acid targets (the reason for miniaturizing hybridization), designing second probes that are specific and that can avoid background hybridization to the immobilized probes becomes extremely difficult, if not impossible. Accordingly, a need exists for improved hybridization in general and for detecting hybridization on microarray formats in particular. The present invention addresses this and other related needs in the art.

SUMMARY OF THE INVENTION

[0010] In one aspect, the present invention provides an oligonucleotide probe for hybridization analysis, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.

[0011] In another aspect, the present invention provides an array of oligonucleotide probes immobilized on a solid support for hybridization analysis, which array comprises a solid support suitable for use in nucleic acid hybridization having immobilized thereon a plurality of oligonucleotide probes, at least one of said probes comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.

[0012] In still another aspect, the present invention provides a method for detecting a target nucleotide sequence in a sample, which method comprises the steps of: a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be detected; b) contacting said probe provided in step a) with a sample containing or suspected of containing said target nucleotide sequence under conditions that favor intermolecular hybridization between said probe and said target nucleotide sequence over intramolecular hybridization of said probe itself; and c) assessing said intermolecular hybrid formed in step b).

[0013] In yet another aspect, the present invention provides a method for transcribing and/or amplifying an oligonucleotide probe sequence, which method comprises the steps of: a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions and contains a promoter sequence, and wherein at least a portion of said nucleotide sequence located within said single stranded loop is complementary to a DNA sequence and said portion of said nucleotide sequence comprises both ribonucleotide sequence and deoxyribonucleotide sequence; b) contacting said probe provided in step a) with said DNA sequence under suitable conditions to form a probe/DNA duplex, preferably without opening said double stranded segment of said probe; c) cleaving said ribonucleotide sequence within said portion of said nucleotide sequence complementary to said DNA sequence by RNase H treatment to open said single stranded loop; and d) synthesizing a RNA sequence using a RNA polymerase that is compatible with said promoter contained within said double stranded segment of said probe, whereby at least a portion of said single stranded loop is transcribed.

BRIEF DESCRIPTION OF THE DRAWINGS

[0014]FIG. 1 illustrates one embodiment of nucleic acid hybridization analysis using an immobilized hairpin probe. SS depicts a solid support upon which the hairpin probe is immobilized. 11, 12, 22 are parts of an immobilized hairpin probe, wherein 11 and 22 forms the double-stranded stem region, 12 is the single-stranded loop region, which can be a non-nucleic acid moiety, and at least a portion of 22 is complementary to the target nucleotide sequence 33. Under suitable conditions, 22 forms a duplex with the target nucleotide sequence 33 and leaves 11 as a single-stranded region. The duplex formed between 22 and 33 is then cleaved off the immobilized probe, preferably with an enzyme, e.g., a RNase H or a restriction enzyme that recognizes a restriction enzyme cleavage site within the duplex. A labeled detecting probe, 44, is hybridized with the single-stranded region 11, which gives a readout signal for detecting hybridization between the hairpin probe and the target nucleotide sequence. If, in the original hybridization step, 22 and 33 are not complementary to each other and do not form a duplex, 11 is still masked by 22 and cannot be hybridized with the detecting probe 44, so no signal is detected.

[0015]FIG. 2 illustrates hairpin probes with multiple single-stranded loop regions. 22, 23 and 24 are complementary to target nucleotide sequence. 12, 23 and 24 can be non-nucleic acid moieties, e.g., linked polyethylene glycols.

[0016]FIG. 3 shows the minimum number of ribonucleotides in DNA/RNA chimeric oligonucleotide for RNase H cleavage. The positions of the oligo alone and the duplex are indicated, respectively. 3A. Lane 1: AGT02008+AGT02009 without RNase H treatment; Lane 2: AGT02008+AGT02009 with RNase H treatment; Lane 3: AGT02012+AGT02009 without RNase H treatment; Lane 4: AGT02012+AGT02009 with RNase H treatment; Lane 5: AGT02013+AGT02009 without RNase H treatment; Lane 6: AGT02013+AGT02009 with RNase H treatment; Lane 7: AGT02014+AGT02009 without RNase H treatment; and Lane 8: AGT02014 +AGT02009 with RNase H treatment. 3B. Lane 1: AGT02008 without RNase H treatment; Lane 2: AGT02008 with RNase H treatment (5 units, 1 hour); Lane 3: AGT02012 without RNase H treatment; Lane 4: AGT02012 with RNase H treatment (5 units, 1 hour); Lane 5: AGT02012 with RNase H treatment (10 units, 1 hour); Lane 6: AGT02012 with RNase H treatment (50 units, 1 hour); Lane 7: AGT02013 without RNase H treatment; Lane 8: AGT02013 with RNase H treatment (5 units, 1 hour); Lane 9: AGT02013 with RNase H treatment (10 units, 1 hour); Lane 10: AGT02013 with RNase H treatment (50 units, 1 hour).

[0017]FIG. 4 shows that mismatch inhibits RNase H activity. The positions of the oligo alone and the duplex are indicated, respectively. 4A. Lane 1: AGT02009 without RNase H treatment; Lane 2: AGT02008+AGT02009 without RNase H treatment; Lane 3: AGT02008+AGT02009 with RNase H treatment; Lane 4: AGT02020 without RNase H treatment; Lane 5: AGT02008+AGT02020 without RNase H treatment; Lane 6: AGT02008+AGT02020 with RNase H treatment; Lane 7: AGT02021 without RNase H treatment; Lane 8: AGT02008+AGT02021 without RNase H treatment; Lane 9: AGT02008+AGT02021 with RNase H treatment; Lane 10: AGT02022 without RNase H treatment; Lane 11: AGT02008+AGT02022 without RNase H treatment; Lane 12: AGT02008+AGT02022 with RNase H treatment; Lane 13: AGT02023 without RNase H treatment; Lane 14: AGT02008+AGT02023 without RNase H treatment; Lane 15: AGT02008+AGT02023 with RNase H treatment. 4B. Lane 1: AGT02008+AGT02009 without RNase H treatment; Lane 2: AGT02008+AGT02009 with RNase H treatment; Lane 3: AGT02008+AGT02021 without RNase H treatment; Lane 4: AGT02008+AGT02021 with RNase H treatment; Lane 5: AGT02008+AGT02024 without RNase H treatment; Lane 6: AGT02008+AGT02024 with RNase H treatment; Lane 7: AGT02008+AGT02025 without RNase H treatment; Lane 8: AGT02008+AGT02025 with RNase H treatment.

[0018]FIG. 5 shows that RNase H can be used in hairpin structure cleavage assay. The positions of the hairpin oligo, the cut out form of the hairpin oligo, the uncut duplex and the target DNA are indicated, respectively. 5A. Lane 1: AGT02010 without RNase H treatment; Lane 2: AGT02010 with RNase H treatment; Lane 3: AGT02010+AGT02028 with RNase H treatment (annealing temperature at 60.2° C.); Lane 4: AGT02010+AGT02028 with RNase H treatment (annealing temperature at 64.5° C.); Lane 5: AGT02010+AGT02028 with RNase H treatment (annealing temperature at 69.6° C.); Lane 6: AGT02010+AGT02028 with RNase H treatment (annealing temperature at 74.8° C.); Lane 7: AGT02010+AGT02028 with RNase H treatment (annealing temperature at 79.9° C.); Lane 8: AGT02010+AGT02028 without RNase H treatment (annealing temperature at 79.9° C.). 5B. Lane 1: AGT02011 without RNase H treatment; Lane 2: AGT02011 with RNase H treatment; Lane 3: AGT02011+AGT02029 with RNase H treatment (annealing temperature at 60.2° C.); Lane 4: AGT02011+AGT02029 with RNase H treatment (annealing temperature at 64.5° C.); Lane 5: AGT02011+AGT02029 with RNase H treatment (annealing temperature at 69.6° C.); Lane 6: AGT02011+AGT02029 with RNase H treatment (annealing temperature at 74.8° C.); Lane 7: AGT02011+AGT02029 with RNase H treatment (annealing temperature at 79.9° C.); Lane 8: AGT02011+AGT02029 without RNase H treatment (annealing temperature at 79.9° C.).

[0019]FIG. 6 shows that the hairpin probe can bind with single strand target oligo at a wide range of temperatures. The positions of the duplex, the hairpin oligo and the target DNA are indicated, respectively. 6A. Lane 1: AGT02010; Lane 2: AGT02028; Lane 3: AGT02010+AGT02028 (annealing temperature at 37° C.); Lane 4: AGT02010+AGT02028 (annealing temperature at 47° C.); Lane 5: AGT02010+AGT02028 (annealing temperature at 55° C.); Lane 6: AGT02010+AGT02028 (annealing temperature at 65° C.); Lane 7: AGT02010+AGT02028 (annealing temperature at 75° C.); Lane 8: AGT02010+AGT02028 (annealing temperature at 85° C.). 6B. Lane 1: AGT02010; Lane 2: AGT02028; Lane 3: AGT02010+AGT02028 (0.25 μg) (annealing temperature at 18° C.); Lane 4: AGT02010+AGT02028 (3 μg) (annealing temperature at 18° C.); Lane 5: AGT02010+AGT02028 (0.25 μg) (annealing temperature at 25° C.); Lane 6: AGT02010+AGT02028 (3 μg) (annealing temperature at 25° C.); Lane 7: AGT02010+AGT02028 (0.25 μg) (annealing temperature at 30° C.); Lane 8: AGT02010+AGT02028 (3 μg) (annealing temperature at 30° C.). 6C. Lane 1: AGT02010; Lane 2: AGT02028; Lane 3: AGT02010+AGT02028 (annealing at room temperature for 1 minute); Lane 4: AGT02010+AGT02028 (annealing at room temperature for 2 minutes); Lane 5: AGT02010+AGT02028 (annealing at room temperature for 3 minutes); Lane 6: AGT02010+AGT02028 (annealing at room temperature for 4 minutes); Lane 7: AGT02010+AGT02028 (annealing at room temperature for 5 minutes); Lane 8: AGT02010+AGT02028 (annealing at 4° C. for 10 minutes).

[0020]FIG. 7 shows the sequence specificity of hairpin probe. The positions of the duplex, the hairpin oligo and the target DNA are indicated, respectively. Lane 1: AGT02011; Lane 2: AGT02029; Lane 3: AGT02011+AGT02029; Lane 4: AGT02039; Lane 5: AGT02011+AGT02039; Lane 6: AGT02040; Lane 7: AGT02011+AGT02040; Lane 8: AGT02011; Lane 9: AGT02048; Lane 10: AGT02011+AGT02048.

[0021]FIG. 8 shows that the loop region of a hairpin probe play an important role in target sequence binding. The positions of the duplex, the hairpin oligo and the target DNA are indicated, respectively. Lane 1: AGT02011; Lane 2: AGT02029; Lane 3: AGT02011+AGT02029; Lane 4: AGT02035; Lane 5: AGT02011+AGT02035; Lane 6: AGT02036; Lane 7: AGT02011+AGT02036.

[0022]FIG. 9 illustrates transcription and/or amplification of an oligonucleotide probe sequence using a hairpin probe. In practice, a hairpin probe having a promoter (circle) in the stem region and ribonucleotide sequence (rectangle) surrounded by deoxyribonucleotide sequence is hybridized with a complementary DNA strand. RNase H can be used to cleave within the ribonucleotide sequence of the duplex to open the single stranded loop of the hairpin probe. Once the loop is opened, a RNA polymerase can be used to transcribe bc region of the opened loop.

DETAILED DESCRIPTION OF THE INVENTION

[0023] The present invention provides probes and methods for nucleic acid hybridization analysis with improved specificity and speed. Central to this goal is the use of probes with a hairpin structure, preferably immobilized to a solid support, that are capable of intramolecular and intermolecular hybridization.

[0024] Intramolecular hybridization of the hairpin probe is accomplished by two complementary sequences in the probe running in opposite directions to each other, such that the bases in each sequence hybridize intramolecularly under the appropriate conditions, forming a double stranded loop within the probe, i.e., a hairpin structure. Intermolecular hybridization of the hairpin probe is accomplished by designing the probes to contain a sequence complementary to the target nucleotide sequence.

[0025] A useful feature of the hairpin probes used herein is the overlap between the probe sequences involved in intramolecular hybridization with the probe sequence involved in hybridizing intermolecularly with a target nucleic acid. By overlapping these sequences, a portion of the hairpin probe has the dual property of being able to engage in intramolecular or intermolecular hybridization. It is through such overlap that background hybridization from the direct or indirect detection method can be reduced and thus improving specificity.

[0026] For clarity of disclosure, and not by way of limitation, the detailed description of the invention is divided into the subsections that follow.

[0027] A. Definitions

[0028] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which this invention belongs. All patents, applications, published applications and other publications and sequences from GenBank and other databases referred to herein are incorporated by reference in their entirety. If a definition set forth in this section is contrary to or otherwise inconsistent with a definition set forth in applications, published applications and other publications and sequences from GenBank and other data bases that are herein incorporated by reference, the definition set forth in this section prevails over the definition that is incorporated herein by reference.

[0029] As used herein, “a” or “an” means “at least one” or “one or more.”

[0030] As used herein, “hairpin structure” refers to a polynucleotide or nucleic acid that contains a double-stranded stem segment and a single-stranded loop segment wherein the two polynucleotide or nucleic acid strands that form the double-stranded stem segment are linked and separated by the single polynucleotide or nucleic acid strand that forms the loop segment. The “hairpin structure” can also further comprise 3′ and/or 5′ single-stranded region(s) extending from the double-stranded stem segment.

[0031] As used herein, “complementary or matched” means that two nucleic acid sequences have at least 50% sequence identity. Preferably, the two nucleic acid sequences have at least 60%, 70,%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% of sequence identity. “Complementary or matched” also means that two nucleic acid sequences can hybridize under low, middle and/or high stringency condition(s).

[0032] As used herein, “substantially complementary or substantially matched” means that two nucleic acid sequences have at least 90% sequence identity. Preferably, the two nucleic acid sequences have at least 95%, 96%, 97%, 98%, 99% or 100% of sequence identity. Alternatively, “substantially complementary or substantially matched” means that two nucleic acid sequences can hybridize under high stringency condition(s).

[0033] As used herein, “two perfectly matched nucleotide sequences” refers to a nucleic acid duplex wherein the two nucleotide strands match according to the Watson-Crick basepair principle, i.e., A-T and C-G pairs in DNA:DNA duplex and A-U and C-G pairs in DNA:RNA or RNA:RNA duplex, and there is no deletion or addition in each of the two strands.

[0034] As used herein, “at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with” means that at least 50% of the nucleotide sequence complementary to the target nucleotide sequence to be detected is located within said double stranded segment and said single stranded loop. Preferably, at least 60%, 70,%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% of the nucleotide sequence complementary to the target nucleotide sequence to be detected is located within said double stranded segment and said single stranded loop.

[0035] As used herein, “conditions that favor intermolecular hybridization between said probe and said target nucleotide sequence over intramolecular hybridization of said probe itself” refers to the conditions under which the intermolecular hybrid can stably exist and be detected while the intramolecular hybrid cannot stably exist and be detected.

[0036] As used herein, “melting temperature” (“Tm”) refers to the midpoint of the temperature range over which nucleic acid duplex, i.e., DNA:DNA, DNA:RNA and RNA:RNA, is denatured.

[0037] As used herein: “stringency of hybridization” in determining percentage mismatch is as follows:

[0038] 1) high stringency: 0.1×SSPE, 0.1% SDS, 65° C.;

[0039] 2) medium stringency: 0.2×SSPE, 0.1% SDS, 50° C. (also referred to as moderate stringency); and

[0040] 3) low stringency: 1.0×SSPE, 0.1% SDS, 50° C.

[0041] It is understood that equivalent stringencies may be achieved using alternative buffers, salts and temperatures (See generally, Ausubel (Ed.) Current Protocols in Molecular Biology, 2.9A. Southern Blotting, 2.9B. Dot and Slot Blotting of DNA and 2.10. Hybridization Analysis of DNA Blots, John Wiley & Sons, Inc. (2000)).

[0042] As used herein, “assessing” refers to quantitative and/or qualitative determination of the intermolecular hybrid formed between the hairpin probe and the target nucleotide sequence, e.g., obtaining an absolute value for the amount or concentration of the intermolecular hybrid, and also of obtaining an index, ratio, percentage, visual or other value indicative of the level of the intermolecular hybrid. Assessment may be direct or indirect and the chemical species actually detected need not of course be the intermolecular hybrid itself but may, for example, be a derivative thereof or some further substance.

[0043] As used herein, a “significant reduction in background hybridization” means that in the absence of a target containing nucleic acid sample, hybridization of the detectably labeled probe with the hairpin probe itself is reduced by at least 80%, more preferably by at least 90%, even more preferably by at least 95%, still more preferably by at least 99%.

[0044] As used herein, “plant” refers to any of various photosynthetic, eucaryotic multi-cellular organisms of the kingdom Plantae, characteristically producing embryos, containing chloroplasts, having cellulose cell walls and lacking locomotion.

[0045] As used herein, “animal” refers to a multi-cellular organism of the kingdom of Animalia, characterized by a capacity for locomotion, nonphotosynthetic metabolism, pronounced response to stimuli, restricted growth and fixed bodily structure. Non-limiting examples of animals include birds such as chickens, vertebrates such fish and mammals such as mice, rats, rabbits, cats, dogs, pigs, cows, ox, sheep, goats, horses, monkeys and other non-human primates.

[0046] As used herein, “tissue” refers to a collection of similar cells and the intracellular substances surrounding them. There are four basic tissues in the body: 1) epithelium; 2) connective tissues, including blood, bone, and cartilage; 3) muscle tissue; and 4) nerve tissue.

[0047] As used herein, “organ” refers to any part of the body exercising a specific function, as of respiration, secretion or digestion.

[0048] As used herein, “disease or disorder” refers to a pathological condition in an organism resulting from, e.g., infection or genetic defect, and characterized by identifiable symptoms.

[0049] As used herein, “neoplasm (neoplasia)” refers to abnormal new growth, and thus means the same as tumor, which may be benign or malignant. Unlike hyperplasia, neoplastic proliferation persists even in the absence of the original stimulus.

[0050] As used herein, “cancer” refers to a general term for diseases caused by any type of malignant tumor.

[0051] As used herein, “an immune system disease or disorder” refers to a pathological condition caused by a defect in the immune system. The immune system is a complex and highly developed system, yet its mission is simple: to seek and kill invaders. If a person is born with a severely defective immune system, death from infection by a virus, bacterium, fungus or parasite will occur. In severe combined immunodeficiency, lack of an enzyme means that toxic waste builds up inside immune system cells, killing them and thus devastating the immune system. A lack of immune system cells is also the basis for DiGeorge syndrome: improper development of the thymus gland means that T cell production is diminished. Most other immune disorders result from either an excessive immune response or an ‘autoimmune attack’. For example, asthma, familial Mediterranean fever and Crohn disease (inflammatory bowel disease) all result from an over-reaction of the immune system, while autoimmune polyglandular syndrome and some facets of diabetes are due to the immune system attacking ‘self’ cells and molecules. A key part of the immune system's role is to differentiate between invaders and the body's own cells—when it fails to make this distinction, a reaction against ‘self’ cells and molecules causes autoimmune disease.

[0052] As used herein, “a metabolism disease or disorder” refers to a pathological condition caused by errors in metabolic processes. Metabolism is the means by which the body derives energy and synthesizes the other molecules it needs from the fats, carbohydrates and proteins we eat as food, by enzymatic reactions helped by minerals and vitamins. There is a significant level of tolerance of errors in the system: often, a mutation in one enzyme does not mean that the individual will suffer from a disease. A number of different enzymes may compete to modify the same molecule, and there may be more than one way to achieve the same end result for a variety of metabolic intermediates. Disease will only occur if a critical enzyme is disabled, or if a control mechanism for a metabolic pathway is affected.

[0053] As used herein, “a muscle and bone disease or disorder” refers to a pathological condition caused by defects in genes important for the formation and function of muscles, and connective tissues. Connective tissue is used herein as a broad term that includes bones, cartilage and tendons. For example, defects in fibrillin—a connective tissue protein that is important in making the tissue strong yet flexible—cause Marfan syndrome, while diastrophic dysplasia is caused by a defect in a sulfate transporter found in cartilage. Two diseases that originate through a defect in the muscle cells themselves are Duchenne muscular dystrophy (DMD) and myotonic dystrophy (DM). DM is another ‘dynamic mutation’ disease, similar to Huntington disease, that involves the expansion of a nucleotide repeat, this time in a muscle protein kinase gene. DMD involves a defect in the cytoskeletal protein, dystrophin, which is important for maintaining cell structure.

[0054] As used herein, “a nervous system disease or disorder” refers to a pathological condition caused by defects in the nervous system including the central nervous system, i.e., brain, and the peripheral nervous system. The brain and nervous system form an intricate network of electrical signals that are responsible for coordinating muscles, the senses, speech, memories, thought and emotion. Several diseases that directly affect the nervous system have a genetic component: some are due to a mutation in a single gene, others are proving to have a more complex mode of inheritance. As our understanding of the pathogenesis of neurodegenerative disorders deepens, common themes begin to emerge: Alzheimer brain plaques and the inclusion bodies found in Parkinson disease contain at least one common component, while Huntington disease, fragile X syndrome and spinocerebellar atrophy are all ‘dynamic mutation’ diseases in which there is an expansion of a DNA repeat sequence. Apoptosis is emerging as one of the molecular mechanisms invoked in several neurodegenerative diseases, as are other, specific, intracellular signaling events. The biosynthesis of myelin and the regulation of cholesterol traffic also figure in Charcot-Marie-Tooth and Neimann-Pick disease, respectively.

[0055] As used herein, “a signal disease or disorder” refers to a pathological condition caused by defects in the signal transduction process. Signal transduction within and between cells mean that they can communicate important information and act upon it. Hormones released from their site of synthesis carry a message to their target site, as in the case of leptin, which is released from adipose tissue (fat cells) and transported via the blood to the brain. Here, the leptin signals that enough has been eaten. Leptin binds to a receptor on the surface of hypothalamus cells, triggering subsequent intracellular signaling networks. Intracellular signaling defects account for several diseases, including cancers, ataxia telangiectasia and Cockayne syndrome. Faulty DNA repair mechanisms are also invoked in pathogenesis, since control of cell division, DNA synthesis and DNA repair all are inextricably linked. The end-result of many cell signals is to alter the expression of genes (transcription) by acting on DNA-binding proteins. Some diseases are the result of a lack of or a mutation in these proteins, which stop them from binding DNA in the normal way. Since signaling networks impinge on so many aspects of normal function, it is not surprising that so many diseases have at least some basis in a signaling defect.

[0056] As used herein, “a transporter disease or disorder” refers to a pathological condition caused by defects in a transporter, channel or pump. Transporters, channels or pumps that reside in cell membranes are key to maintaining the right balance of ions in cells, and are vital for transmitting signals from nerves to tissues. The consequences of defects in ion channels and transporters are diverse, depending on where they are located and what their cargo is. For example, in the heart, defects in potassium channels do not allow proper transmission of electrical impulses, resulting in the arrhythmia seen in long QT syndrome. In the lungs, failure of a sodium and chloride transporter found in epithelial cells leads to the congestion of cystic fibrosis, while one of the most common inherited forms of deafness, Pendred syndrome, looks to be associated with a defect in a sulphate transporter.

[0057] As used herein, “infection” refers to invasion of the body of a multi-cellular organism with organisms that have the potential to cause disease.

[0058] As used herein, “infectious organism” refers to an organism that is capable to cause infection of a multi-cellular organism. Most infectious organisms are microorganisms such as viruses, bacteria and fungi.

[0059] As used herein, “bacteria” refers to small prokaryotic organisms (linear dimensions of around 1 μm) with non-compartmentalized circular DNA and ribosomes of about 70S. Bacteria protein synthesis differs from that of eukaryotes. Many anti-bacterial antibiotics interfere with bacteria proteins synthesis but do not affect the infected host.

[0060] As used herein, “eubacteria” refers to a major subdivision of the bacteria except the archaebacteria. Most Gram-positive bacteria, cyanobacteria, mycoplasmas, enterobacteria, pseudomonas and chloroplasts are eubacteria. The cytoplasmic membrane of eubacteria contains ester-linked lipids; there is peptidoglycan in the cell wall (if present); and no introns have been discovered in eubacteria.

[0061] As used herein, “archaebacteria” refers to a major subdivision of the bacteria except the eubacteria. There are 3 main orders of archaebacteria: extreme halophiles, methanogens and sulphur-dependent extreme thermophiles. Archaebacteria differs from eubacteria in ribosomal structure, the possession (in some case) of introns, and other features including membrane composition.

[0062] As used herein, “virus” refers to obligate intracellular parasites of living but non-cellular nature, consisting of DNA or RNA and a protein coat. Viruses range in diameter from about 20 to about 300 nm. Class I viruses (Baltimore classification) have a double-stranded DNA as their genome; Class II viruses have a single-stranded DNA as their genome; Class III viruses have a double-stranded RNA as their genome; Class IV viruses have a positive single-stranded RNA as their genome, the genome itself acting as mRNA; Class V viruses have a negative single-stranded RNA as their genome used as a template for mRNA synthesis; and Class VI viruses have a positive single-stranded RNA genome but with a DNA intermediate not only in replication but also in mRNA synthesis. The majority of viruses are recognized by the diseases they cause in plants, animals and prokaryotes. Viruses of prokaryotes are known as bacteriophages.

[0063] As used herein, “fungi” refers to a division of eucaryotic organisms that grow in irregular masses, without roots, stems, or leaves, and are devoid of chlorophyll or other pigments capable of photosynthesis. Each organism (thallus) is unicellular to filamentous, and possess branched somatic structures (hyphae) surrounded by cell walls containing glucan or chitin or both, and containing true nuclei.

[0064] As used herein, “a promoter, a promoter region or promoter element” refers to a segment of DNA or RNA that controls transcription of the DNA or RNA to which it is operatively linked. The promoter region includes specific sequences that are sufficient for RNA polymerase recognition, binding and transcription initiation. This portion of the promoter region is referred to as the promoter. In addition, the promoter region includes sequences that modulate this recognition, binding and transcription initiation activity of RNA polymerase. These sequences may be cis acting or may be responsive to trans acting factors. Promoters, depending upon the nature of the regulation, may be constitutive or regulated.

[0065] As used herein, “operatively linked or operationally associated” refers to the functional relationship of DNA with regulatory and effector sequences of nucleotides, such as promoters, enhancers, transcriptional and translational stop sites, and other signal sequences. For example, operative linkage of DNA to a promoter refers to the physical and functional relationship between the DNA and the promoter such that the transcription of such DNA is initiated from the promoter by an RNA polymerase that specifically recognizes, binds to and transcribes the DNA. In order to optimize expression and/or in vitro transcription, it may be necessary to remove, add or alter 5′ untranslated portions of the clones to eliminate extra, potential inappropriate alternative translation initiation (i.e., start) codons or other sequences that may interfere with or reduce expression, either at the level of transcription or translation. Alternatively, consensus ribosome binding sites (see, e.g., Kozak, J. Biol. Chem., 266:19867-19870 (1991)) can be inserted immediately 5′ of the start codon and may enhance expression. The desirability of (or need for) such modification may be empirically determined.

[0066] As used herein, “RNA polymerase” refers to an enzyme that synthesizes RNA using a DNA or RNA as the template. It is intended to encompass any RNA polymerase with conservative amino acid substitutions that do not substantially alter its activity.

[0067] As used herein, “reverse transcriptase” refers to an enzyme that synthesizes DNA using a RNA as the template. It is intended to encompass any reverse transcriptase with conservative amino acid substitutions that do not substantially alter its activity.

[0068] B. Oligonucleotide Probe Containing a Hairpin Structure

[0069] In one aspect, the present invention provides an oligonucleotide probe for hybridization analysis, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.

[0070] The probe can comprise any kind of oligonucleotide or nucleic acid strand(s) containing genetically-coded and/or naturally occurring structures. The hairpin probes used herein can comprise DNA, RNA, or a combination of DNA and RNA. Hairpin probes also can comprise non-natural elements such as non-natural bases, e.g., inosine and xanthine, non-natural sugars, e.g., 2′-methoxy ribose, or non-natural phosphodiester linkages, e.g., methylphosphonates, phosphorothioates and peptides. For example, in one embodiment of the invention, hairpin probes comprising both DNA and RNA are designed such that DNA of the probe contains a sequence of nucleotides that are complementary to an RNA sequence of the probe running in opposite directions, such that upon intramolecular hybridization, the double stranded portion of the hairpin probe has DNA hybridized to RNA. Alternatively, or in addition, one or both of the complementary sequences of the intramolecularly hybridizing portion of the hairpin probe can be made resistant to a particular nuclease. For example, a methylphosphonate DNA sequence is resistant to cleavage by RNase H. In one specific embodiment, the probe comprises DNA, RNA, PNA or a derivative thereof. In another specific embodiment, the probe comprises both DNA and RNA or derivatives thereof.

[0071] The portion of the nucleotide sequences located within the double stranded segment and the single stranded loop can be substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence. Preferably, the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence.

[0072] The single stranded loop of the probe must contain more than 2 nucleotides. For example, The single stranded loop of the probe can comprise at least 3, 4, 5, 6, 7, 8, 9, 10, 15 or more nucleotides.

[0073] The double stranded segment of the hairpin structure can be formed between two perfectly matched nucleotide sequences or two substantially matched nucleotide sequences.

[0074] The probe can further comprise an element or a modification that facilitates intramolecular crosslinking of the probe upon suitable treatment. Such an element can be a chemically or photoactively activatable crosslinking agent, e.g., furocoumarins. Alternatively, such element can be a macromolecule having multiple ligand binding sites, e.g., component(s) of biotin-avidin binding system or an antigen-antibody binding system.

[0075] The probe can further comprise an element or a modification that renders the probe sensitive or resistant to nuclease digestion. For example, such an element can be a restriction enzyme cleavage site. In another example, at least a portion of the double stranded segment of the probe is a duplex between a DNA strand and a RNA strand, said DNA strand contains methylphosphonates and at least a portion of said RNA strand is complementary to a target nucleotide sequence to be detected. The methylphosphonate DNA:RNA hybrid in the probe itself is resistant to RNase H cleavage. However, once the probe hybridizes with a target DNA sequence, the RNA strand in the formed RNA:DNA duplex can be removed with RNase H treatment.

[0076] Probe sequences that are designed to hybridize intramolecularly or intermolecularly should be sufficiently complementary to hybridize under the selected conditions. Sufficient complementarity exists when an RNA or DNA strand will hybridize under selective hybridization conditions to its complement. Typically, selective hybridization will occur when there is at least about 65% complementarity over a stretch of at least 14 to 25 nucleotides, preferably at least about 75%, more preferably at least about 90% complementarity (See e.g., Kanehisa, Nucleic Acids Res., 12:203 (1984)).

[0077] The intramolecular hybridization sequences in the hairpin probe can be separated by a flexible linker essentially as described in U.S. Pat. No. 5,556,752 to Lockhart et al. Briefly, the flexible linker is chosen to be of sufficient length and of sufficient materials to enable effective intramolecular probe hybridization. The length of the linker will typically be a length which is at least the length spanned by two nucleotide monomers, and preferably at least four nucleotide monomers, while not being so long as to interfere with either the pairing of the complementary (anti-parallel) intramolecularly hybridizing probe sequences. The flexible linker can be DNA, RNA or any of a variety of chemical structures.

[0078] A hairpin probe can be prepared by synthesizing a single polynucleotide. Alternatively, one can separately synthesize each portion of the probe involved in intramolecular hybridization and then couple the portions together as a single hairpin probe by conjugation to each end of a separately prepared flexible linker. In this case, the flexible linker includes a linking group typically an alkylene group (of from about 6 to about 24 carbons in length), a polyethyleneglycol group (of from about 2 to about 24 ethyleneglycol monomers in a linear configuration), a polyalcohol group, a polyamine group (e.g., spermine, spermidine and polymeric derivatives thereof), a polyester group (e.g., poly(ethyl acrylate) having from about 3 to 15 ethyl acrylate monomers in a linear configuration), a polyphosphodiester group, or a polynucleotide (having from about 2 to about 12 nucleic acids). Preferably, the linking group will be a polyethyleneglycol group which is at least a tetraethyleneglycol, and more preferably, from about 1 to 4 hexaethyleneglycols linked in a linear array.

[0079] When synthesizing the hairpin probe from a separate flexible linker and separate intrahybridizing sequence portions of the hairpin probe, the flexible linker will be provided with functional groups at each end that can be suitably protected or activated. The functional groups are covalently attached to each portion of the probe via an ether, ester, carbamate, phosphate ester or amine linkage to either the 5′-hydroxyl or the 3′-hydroxyl of the probe portions chosen such that the complementary intramolecularly hybridizing sequences are in an anti-parallel configuration. Preferred linkages are phosphate ester linkages similar to typical oligonucleotide linkages. For example, hexaethyleneglycol can be protected on one terminus with a photolabile protecting group (i.e., NVOC or MeNPOC) and activated on the other terminus with 2-cyanoethyl-N,N-diisopropylamino-chlorophosphite to form a phosphoramidite. This linking group can then be used for construction of the probe libraries in the same manner as photolabile-protected, phosphoramidite-activated nucleotides. Other methods of forming ether, carbamate or amine linkages are known to those of skill in the art and particular reagents and references can be found in such texts as March, Advanced Organic Chemistry, 4th Ed., Wiley-Interscience, New York, N.Y., 1992.

[0080] Alternatively, naturally occurring oligonucleotides, or fragments thereof, may be isolated from their natural sources or purchased from commercial sources. Probe oligonucleotides can be generally be from nucleotides in length, preferably from about 6 to about 50 nucleotides, although oligonucleotides of different length may be appropriate. Suitable oligonucleotides may be prepared by the phosphoramidite method described by Beaucage and Carruthers, Tetrahedron Lett., 22:1859-1862 (1981), or by the triester method according to Matteucci et al., J. Am. Chem. Soc., 103:3185 (1981), or by other chemical methods using either a commercial automated oligonucleotide synthesizer or by VLSIPS™ technology (discussed in detail below).

[0081] C. Array of Oligonucleotide Probes Containing Hairpin Structures

[0082] In another aspect, the present invention provides an array of oligonucleotide probes immobilized on a solid support for hybridization analysis, which array comprises a solid support suitable for use in nucleic acid hybridization having immobilized thereon a plurality of oligonucleotide probes, at least one of the probes comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.

[0083] Preferably, at least a quarter, a half, two-thirds or each and all of the probes in the array comprise a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains more than 2 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.

[0084] The plurality of probes can comprise DNAs, RNAs, derivatives thereof, or combinations thereof as described in the above Section B. In one specific embodiment, the probe comprises DNA, RNA, PNA or a derivative thereof. In another specific embodiment, the probe comprises both DNA and RNA or derivatives thereof.

[0085] The portion of the nucleotide sequences located within the double stranded segment and the single stranded loop of at least one of the probes can be substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence. Alternatively, the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop of at least one of the probes can be a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence.

[0086] The single stranded loop of at least one of the probes must comprise more than 2 nucleotides. For example, the single stranded loop of at least one of the probes comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 15 or more nucleotides.

[0087] The double stranded segment of the hairpin structure of at least one of the probes can be formed between two perfectly matched nucleotide sequences or two substantially matched nucleotide sequences.

[0088] The probes within an array can further comprise an element or modification that facilitates intramolecular crosslinking of the probes upon suitable treatment, and/or an element or modification that renders the probe sensitive or resistant to nuclease digestion, as described in the above Section B.

[0089] In one specific embodiment, at least one of the probes further comprises an element or modification that facilitates intramolecular crosslinking of the probes upon suitable treatment. Preferably, the element is a chemically or photoactively activatable crosslinking agent, e.g., a furocoumarin.

[0090] In another specific embodiment, the element is a macromolecule having multiple ligand binding sites, e.g., a component of biotin-avidin binding system.

[0091] In still another specific embodiment, at least one of the probes further comprises an element or modification that renders the probe sensitive or resistant to nuclease digestion, e.g., a restriction enzyme cleavage site.

[0092] In yet another specific embodiment, at least a portion of the double stranded segment of at least one of the probes is a duplex between a DNA strand and a RNA strand, said DNA strand contains methylphosphonates and at least a portion of said RNA strand is complementary to a target nucleotide sequence to be detected.

[0093] In yet another specific embodiment, each of the oligonucleotide probes is capable of forming a target nucleotide sequence/oligonucleotide probe duplex with a different target nucleotide sequence.

[0094] Immobilization of Hairpin Probes

[0095] Hairpin probes are preferably immobilized to a solid support such as biochip. The solid support may be biological, nonbiological, organic, inorganic, or a combination of any of these, existing as particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, etc.

[0096] A solid support for immobilizing probes is preferably flat, but may take on alternative surface configurations. For example, the solid support may contain raised or depressed regions on which probe synthesis takes place or where probes are attached. In some embodiments, the solid support can be chosen to provide appropriate light-absorbing characteristics. For example, the support may be a polymerized Langmuir Blodgett film, glass or functionalized glass, Si, Ge, GaAs, GaP, SiO₂, SiN₄, modified silicon, or any one of a variety of gels or polymers such as (poly)tetrafluoroethylene, (poly)vinylidendifluoride, polystyrene, polycarbonate, or combinations thereof. Other suitable solid support materials will be readily apparent to those of skill in the art.

[0097] The surface of the solid support can contain reactive groups, which could be carboxyl, amino, hydroxyl, thiol, or the like suitable for conjugating to a reactive group associated with an oligonucleotide or a nucleic acid. Preferably, the surface is optically transparent and will have surface Si—OH functionalities, such as are found on silica surfaces.

[0098] Hairpin probes can be attached to the solid support by chemical or physical means such as through ionic, covalent or other forces well known in the art. Immobilization of nucleic acids and oligonucleotides can be achieved by means well known in the art (see, e.g., Dattagupta et al., Analytical Biochemistry, 177:85-89(1989); Saiki et al., Proc. Natl. Acad. Sci. USA, 86:6230-6234(1989); and Gravitt et al., J. Clin. Micro., 36:3020-3027(1998)).

[0099] Hairpin probes can be attached to a solid support by means of a spacer molecule, e.g., essentially as described in U.S. Pat. No. 5,556,752 to Lockhart et al., to provide space between the double stranded portion of the probe as may be helpful in hybridization assays. A spacer molecule typically comprises between 6-50 atoms in length and includes a surface attaching portion that attaches to the solid support. Attachment to the support can be accomplished by carbon-carbon bonds using, for example, supports having (poly)trifluorochloroethylene surfaces, or preferably, by siloxane bonds (using, for example, glass or silicon oxide as the solid support). Siloxane bonding can be formed by reacting the support with trichlorosilyl or trialkoxysilyl groups of the spacer. Aminoalkylsilanes and hydroxyalkylsilanes, bis(2-hydroxyethyl)-aminopropyltriethoxysilane, 2-hydroxyethylaminopropyltriethoxysilane, aminopropyltriethoxysilane or hydroxypropyltriethoxysilane are useful are surface attaching groups.

[0100] The spacer can also include an extended portion or longer chain portion that is attached to the surface attaching portion of the probe. For example, amines, hydroxyl, thiol, and carboxyl groups are suitable for attaching the extended portion of the spacer to the surface attaching portion. The extended portion of the spacer can be any of a variety of molecules which are inert to any subsequent conditions for polymer synthesis. These longer chain portions will typically be aryl acetylene, ethylene glycol oligomers containing 2-14 monomer units, diamines, diacids, amino acids, peptides, or combinations thereof.

[0101] In some embodiments, the extended portion of the spacer is a polynucleotide or the entire spacer can be a polynucleotide. The extended portion of the spacer also can be constructed of polyethyleneglycols, polynucleotides, alkylene, polyalcohol, polyester, polyamine, polyphosphodiester and combinations thereof. Additionally, for use in synthesis of probes, the spacer can have a protecting group, attached to a functional group, e.g., hydroxyl, amino or carboxylic acid) on the distal or terminal end of the spacer (opposite the solid support). After deprotection and coupling, the distal end can be covalently bound to an oligomer or probe.

[0102] Microarray Formation

[0103] A variety of hairpin probes can be attached to a single solid support to form a microarray by procedures well known in the art. This is also referred to as a “microarray biochip” or “nucleic acid biochip” or “DNA biochip.”

[0104] A microarry biochip containing a library of probes can be prepared by a number of well known approaches including, for example, light-directed methods, such as VLSIPS™ described in U.S. Pat. No. 5,143,854, 5,384,261 or 5,561,071; bead based methods such as described in U.S. Pat. No. 5,541,061; and pin based methods such as detailed in U.S. Pat. No. 5,288,514. U.S. Pat. No. 5,556,752 to Lockhart, which details the preparation of a library of different double stranded probes as a microarry using the VLSIPS™ also is suitable for preparing a library of hairpin probes in a microarray.

[0105] Flow channel methods, such as described in U.S. Pat. Nos. 5,677,195 and 5,384,261, can be used to prepare a microarry biochip having a variety of different hairpin probes. In this case, certain activated regions of the substrate are mechanically separated from other regions when the probes are delivered through a flow channel to the support. A detailed description of the flow channel method can be found in U.S. Pat. No. 5,556,752 to Lockhart et al., including the use of protective coating wetting facilitators to enhance the directed channeling of liquids though designated flow paths.

[0106] Spotting methods also can be used to prepare a microarry biochip with a variety of hairpin probes immobilized thereon. In this case, reactants are delivered by directly depositing relatively small quantities in selected regions of the support. In some steps, of course, the entire support surface can be sprayed or otherwise coated with a particular solution. In particular formats, a dispenser moves from region to region, depositing only as much probe or other reagent as necessary at each stop. Typical dispensers include a micropipette, nanopippette, ink-jet type cartridge or pin to deliver the probe containing solution or other fluid to the support and, optionally, a robotic system to control the position of these delivery devices with respect to the support. In other formats, the dispenser includes a series of tubes or multiple well trays, a manifold, and an array of delivery devices so that various reagents can be delivered to the reaction regions simultaneously. Spotting methods are well known in the art and include, for example those described in U.S. Pat. Nos. 5,288,514, 5,312,233 and 6,024,138. In some cases, a combination of flowing channel and “spotting” on predefined regions of the support also can be used to prepare microarry biochips with immobilized hairpin probes.

[0107] D. Methods for Detecting a Target Nucleotide Sequence in a Sample

[0108] In still another aspect, the present invention provides a method for detecting a target nucleotide sequence in a sample, which method comprises the steps of: a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be detected; b) contacting the probe provided in step a) with a sample containing or suspected of containing the target nucleotide sequence under conditions that favor intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself; and c) assessing the intermolecular hybrid formed in step b).

[0109] Probes Used in the Method

[0110] To be used in the present methods, at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop must collectively form a region that is complementary to a target nucleotide sequence to be detected. Preferably, the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence. Also preferably, the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence.

[0111] The single stranded loop of the probe must contain more than 2 nucleotides. For example, The single stranded loop of the probe can comprise at least 3, 4, 5, 6, 7, 8, 9, 10, 15 or more nucleotides.

[0112] Hybridization Conditions

[0113] Any conditions that favor intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself can be used in the present methods. Preferably, the conditions that favor intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself is achieved by controlling compositions of the probe and the target nucleotide sequence so that the Tm of the intermolecular hybrid is higher than the Tm of the intramolecular hybrid.

[0114] The intermolecular hybrid can be a RNA:DNA, RNA:RNA or a DNA:DNA hybrid or a derivative thereof and the intramolecular hybrid can be a RNA:DNA, RNA:RNA or a DNA:DNA hybrid or a derivative thereof, provided that a condition favoring intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself can be used. In one example, the intermolecular hybrid is a RNA:RNA hybrid, the intramolecular hybrid is a RNA:DNA or a DNA:DNA hybrid. In another example, the intermolecular hybrid is a RNA:DNA hybrid, the intramolecular hybrid is a DNA:DNA hybrid. Normally, the Tm of the intermolecular hybrid is at least 2° C. higher than the Tm of the intramolecular hybrid. Preferably, the Tm of the intermolecular hybrid is at least 5° C. higher than the Tm of the intramolecular hybrid.

[0115] The hybridization between the hairpin probe and the target nucleotide sequence can be carried out under suitable stringencies, including high, middle or low stringency.

[0116] The hybridization between the hairpin probe and the target nucleotide sequence can be carried out at any suitable temperature. For example, the oligonucleotide probe and the target nucleotide sequence can be contacted at a temperature from about 4° C. to about 90° C. Preferably, the oligonucleotide probe and the target nucleotide sequence can be contacted at a temperature from about 25° C. to about 60° C. More preferably, the oligonucleotide probe and the target nucleotide sequence can be contacted at a temperature from about 35° C. to about 50° C.

[0117] The hybridization between the hairpin probe and the target nucleotide sequence can be carried out for any suitable period of time. For example, the oligonucleotide probe and the target nucleotide sequence can be contacted for a time from about 1 minute to about 60 minutes. Preferably, the oligonucleotide probe and the target nucleotide sequence can be contacted for a time from about 15 minutes to about 30 minutes.

[0118] Detection of the Intermolecular Hybrid

[0119] Any suitable methods can be used in detecting the intermolecular hybrid formed between the probe and the target nucleotide sequence. For example, the direct labeling approach can be used, e.g., the target nucleotide sequence is detectably labeled and the formation of the intermolecular hybrid is assessed by detecting the label of the target nucleotide sequence in the intermolecular hybrid. Any suitable label can be used, including a chemical, an enzymatic, an radioactive, a fluorescent, a luminescent and a FRET (fluorescence resonance energy transfer) label. The luminescent label can be a chemiluminescent label, e.g., acridinium ester, or a bioluminescent label.

[0120] The indirect labeling approach can also be used, i.e., the formation of the intermolecular hybrid is assessed by addition of a detectably labeled secondary probe that specifically hybridizes with at least a portion of the intermolecular hybrid and the detection of a secondary intermolecular hybrid formed between the secondary probe and the original intermolecular hybrid indicates the presence of said target nucleotide sequence in said sample.

[0121] When such indirect labeling approach is used, the method preferably further comprises a step of crosslinking the intermolecular hybrid and the intramolecular hybrid after the formation of the intermolecular hybrid but before the addition of the detectably labeled secondary probe. Any crosslinking method can used. For example, the crosslinking step can be effected via addition of a crosslinking agent subsequent to hybridization of the original probe with the target nucleotide sequence. Alternatively, the original hairpin probe can be synthesized with the crosslinking agent attached and crosslinking can be achieved by addition of an appropriate agent or treatment.

[0122] In one specific embodiment, the secondary probe specifically hybridizes with a portion of the target nucleotide sequence that is not involved in the hybridization of the target nucleotide sequence and the original probe.

[0123] In another specific embodiment, the secondary probe specifically hybridizes with a portion of the target nucleotide sequence that is involved in the hybridization of the target nucleotide sequence and the original probe and the nucleotide sequence in the original probe that is complementary to the same portion of the target nucleotide sequence is removed prior to or concurrently with the addition of the secondary probe. Many strategies can be used to ensure that the nucleotide sequence in the original probe that is complementary to the same portion of the target nucleotide sequence is removed prior to or concurrently with the addition of the secondary probe. For example, the hairpin structure in the original probe can be formed between a DNA strand that contains methylphosphonates and a RNA strand that is complementary to the target nucleotide sequence and wherein the RNA strand, after forming a hybrid with the target nucleotide sequence but before the addition of the secondary probe, is removed by a RNase H treatment.

[0124] In still another specific embodiment, the secondary probe specifically hybridizes with a portion of the original probe that is involved in the formation of the intramolecular hybrid but is not involved in the formation of the intermolecular hybrid with the target nucleotide sequence and wherein the same portion of the original probe that remains within the unhybridized original probe is removed prior to or concurrently with the addition of the secondary probe. Many strategies can be used to ensure that the same portion of the original probe that remains within the unhybridized original probe is removed prior to or concurrently with the addition of the secondary probe. For example, the portion of the original probe that remains within the unhybridized original probe contains a restriction enzyme cleavage site and is removed by cleavage with said restriction enzyme.

[0125] When detecting hybridization by an indirect detection method, a detectably labeled second probe(s) can be added after initial hybridization between the hairpin probe and the target or during hybridization of the hairpin probe and the target. When the labeled secondary probe is added after an initial hybridization reaction between the hairpin probe and the target, optionally, the immobilized hairpin probes can be subject to hybridization conditions that induce intramolecular hybridization of any non-intermolecularly hybridized hairpin probe. In this case, background hybridization between non-intermolecularly hybridized hairpin probe and a detectably labeled second probe is reduced upon subsequent hybridization.

[0126] After hybridization, unhybridized secondary probe can be separated from the hairpin probe by, for example, by washing if the hairpin probe is immobilized on a solid support. In the case of a solid support, detection of label bound to locations on the support indicates intermolecular hybridization of a target nucleotide sequence in the sample to the hairpin probe.

[0127] Secondary Probe

[0128] The detectably labeled secondary probe can be a specific probe. Alternatively, the detectably labeled probe can be a degenerate probe, e.g., a mixture of sequences such as whole genomic DNA essentially as described in U.S. Pat. No. 5,348,855. In the latter case, labeling can be conducted through use of intercalating dyes if the secondary probe contains double stranded DNA.

[0129] A secondary probe also can be a library of random nucleotide probe sequences. The length of a secondary probe should be decided in view of the length and composition of the primary probe or the target nucleotide sequence on the solid support that is to be detected by the secondary probe. Such a probe library is preferably provided with a 3′ or 5′ end labeled with photoactivatable reagent and the other end loaded with a detection reagent such as a fluorophore, enzyme, dye, luminophore, or other detectably known moiety.

[0130] The secondary probe can be detectably labeled by methods well known in the art including, for example, radioisotope, fluorophore, enzyme, dye, luminophore, or other detectably known moiety (See e.g., U.S. Pat. No. 5,348,855). For example, a variety of DNA-binding ligands are known to be useful for linking a nucleic acid secondary probe to a detectable the label. Particularly preferred DNA-binding ligands are intercalator compounds such as the furocoumarins, e.g., angelicin (isopsoralen) or psoralen or derivatives thereof, which photochemically react with nucleic acids, e.g., 4′-aminomethyl-4,5′-dimethylangelicin, 4′-aminomethyl-trioxsalen (4′aminomethyl-4,5′,8-trimethyl-psoralen), 3-carboxy-5- or -8-amino- or-hydroxy-psoralen, as well as mono- or bis-azido aminoalkyl methidium or ethidium compounds.

[0131] Particularly useful photoreactive forms of intercalating agents are the azidointercalators. Their reactive nitrenes are readily generated at long wavelength ultraviolet or visible light and the nitrenes of arylazides prefer insertion reactions over their rearrangement products (White et al., Meth. Enzymol., 46:644 (1977)). Representative intercalating agents include azidoacridine, ethidium monoazide, ethidium diazide, ethidium dimer azide (Mitchell et al., J. Am. Chem. Soc., 104:4265 (1982)), 4-azido-7-chloroquinoline, and 2-azidofluorene. A specific nucleic acid binding azido compound has been described by Forster et al., Nucleic Acid Res., 13:745 (1985). Other useful photoreactable intercalators are the furocoumarins which form (2+2) cycloadducts with pyrimidine residues. Alkylating agents also can be used as the DNA binding ligand, including, for example, bis-chloroethylamines and epoxides or aziridines, e.g., aflatoxins, polycyclic hydrocarbon epoxides, mitomycin and norphillin A.

[0132] Particularly useful labels are enzymatically active groups such as enzymes (Wisdom, Clin. Chem., 22:1243 (1976)); enzyme substrates (British Pat. No. 1,548,741); coenzymes (U.S. Pat. Nos. 4,230,797 and 4,238,565) and enzyme inhibitors (U.S. Pat. No. 4,134,792); fluorescers (Soini and Hemmila, Clin. Chem., 25:353 (1979)); chromophores including phycobiliproteins, luminescers such as chemiluminescers and bioluminescers (Gorus and Schram, Clin. Chem., 25:512 (1979) and ibid, 1531); specifically bindable ligands, i.e., protein binding ligands; antigens; and residues comprising radioisotopes such as ³H, ³⁵S, ³²P, ¹²⁵I, and ¹⁴C. Such labels are detected on the basis of their own physical properties (e.g., fluorescers, chromophores and radioisotopes) or their reactive or binding properties (e.g., enzymes, substrates, coenzymes and inhibitors).

[0133] For example, a cofactor-labeled nucleic acid can be detected by adding the enzyme for which the label is a cofactor and a substrate for the enzyme. A hapten or ligand (e.g., biotin) labeled nucleic acid can be detected by adding an antibody or an antibody pigment to the hapten or a protein that binds the ligand (e.g., avidin), tagged with a detectable molecule. A detectable molecule has a measurable physical property (e.g., fluorescence or absorbance) or is participant in an enzyme reaction (e.g., see above list). For example, one can use an enzyme which acts upon a substrate to generate a product with a measurable physical property. Examples of the latter include, but are not limited to, beta-galactosidase, alkaline phosphatase, papain and peroxidase. For in situ hybridization studies, the final product of the substrate is preferably water insoluble. Other labels, e.g., dyes, will be evident to one having ordinary skill in the art.

[0134] If the label is an enzyme, the labeled DNA is ultimately placed in a suitable medium to determine the extent of catalysis. Thus, if the enzyme is a phosphatase, the medium can contain nitrophenyl phosphate and one can monitor the amount of nitrophenol generated by observing the color. If the enzyme is a beta-galactosidase, the medium can contain o-nitro-phenyl-D-galacto-pyranoside, which also liberates nitrophenol. The label can be linked to the DNA binding ligand, e.g., acridine dyes, phenanthridines, phenazines, furocoumarins, phenothiazines and quinolines, by direct chemical linkage such as involving covalent bonds, or by indirect linkage such as by the incorporation of the label in a microcapsule or liposome, which in turn is linked to the binding ligand. Methods by which the label is linked to a DNA binding ligand such as an intercalator compound are well known in the art and any convenient method can be used.

[0135] Advantageously, the DNA binding ligand is first combined with label chemically and thereafter combined with the nucleic acid secondary probe. For example, since biotin carries a carboxyl group, it can be combined with a furocoumarin by way of amide or ester formation without interfering with the photochemical reactivity of the furocoumarin or the biological activity of the biotin. Aminomethylangelicin, psoralen and phenanthridium derivatives can similarly be linked to a label, as can phenanthridium halides and derivatives thereof such as aminopropyl methidium chloride (Hertzberg et al, J. Amer. Chem. Soc., 104:313 (1982)). Alternatively, a bifunctional reagent such as dithiobis succinimidyl propionate or 1,4-butanediol diglycidyl ether can be used directly to couple the DNA binding ligand to the label where the reactants have alkyl amino residues, again in a known manner with regard to solvents, proportions and reaction conditions. Certain bifunctional reagents, possibly glutaraldehyde may not be suitable because, while they couple, they may modify nucleic acid and thus interfere with the assay. Routine precautions can be taken to prevent such difficulties.

[0136] The particular sequence used in making the labeled nucleic acid can be varied. Thus, for example, an amino-substituted psoralen can first be photochemically coupled with a nucleic acid, the product having pendant amino groups by which it can be coupled to the label, i.e., labeling is carried out by photochemically reacting a DNA binding ligand with the nucleic acid in the test sample. Alternatively, the psoralen can first be coupled to a label such as an enzyme and then to the nucleic acid.

[0137] Also advantageously, the DNA binding ligand can be linked to the label by a spacer, which includes a chain of up to about 40 atoms, preferably about 2 to 20 atoms, including, but not limited to, carbon, oxygen, nitrogen and sulfur. Such spacer can be the polyfunctional radical of a member including, but not limited to, peptide, hydrocarbon, polyalcohol, polyether, polyamine, polyimine and carbohydrate, e.g., -glycyl-glycyl-glycyl- or other oligopeptide, carbonyl dipeptides, and omega-amino-alkane-carbonyl radical or the like. Sugar, polyethylene oxide radicals, glyceryl, pentaerythritol, and like radicals also can serve as spacers. Spacers can be directly linked to the nucleic acid-binding ligand and/or the label, or the linkages may include a divalent radical of a coupler such as dithiobis succinimidyl propionate, 1,4-butanediol diglycidyl ether, a diisocyanate, carbodiimide, glyoxal, glutaraldehyde, or the like.

[0138] The detectable label can be visualized or assessed by placing the probe array next to x-ray film or phosphorimagers to identify the sites where the secondary probe has bound. Fluorescence can be detected by way of a charge-coupled device (CCD) or laser scanning.

[0139] The detectably labeled secondary probe(s) can be added after hybridization or during hybridization of the test sample to the hairpin probe. Optionally the hybridization conditions may be modified after addition of the secondary probe. After hybridization, unhybridized secondary probe is separated from the hairpin probe by, for example, washing if the hairpin probe is immobilized on a solid support. In the case of a solid support, detection of label bound to locations on the support indicates intermolecular hybridization of a target nucleotide sequence in the sample to the hairpin probe.

[0140] A secondary probe for indirect detection of hybridization can be detected by energy transfer such as in the “beacon probe” method described by Tyagi and Kramer, Nature Biotech., 14:303-309 (1996) or U.S. Pat. Nos. 5,119,801 and 5,312,728 to Lizardi et al. The secondary probes used herein can be a hairpin probe with a donor fluorophore at one end of the probe and an acceptor moiety, usually a quencher, at the other end of the probe. Thus when the secondary probe is in the open conformation, the fluorescence of the donor fluorophore is detectable, whereas when the second probe is in a hairpin or closed conformation, the fluorescence of the donor fluorophore is quenched.

[0141] Any FRET detection system known in the art can be used in the present method. For example, the AlphaScreen™ system can be used. AlphaScreen technology is an “Amplified Luminescent Proximity Homogeneous Assay” method. Upon illumination with laser light at 680 nm, a photosensitizer in the donor bead converts ambient oxygen to singlet-state oxygen. The excited singlet-state oxygen molecules diffuse approximately 250 nm (one bead diameter) before rapidly decaying. If the acceptor bead is in close proximity of the donor bead, by virtue of a biological interaction, the singlet-state oxygen molecules reacts with chemiluminescent groups in the acceptor beads, which immediately transfer energy to fluorescent acceptors in the same bead. These fluorescent acceptors shift the emission wavelength to 520-620 nm. The whole reaction has a 0.3 second half-life of decay, so measurement can take place in time-resolved mode. Other exemplary FRET donor/acceptor pairs include Fluorescein (donor) and tetramethylrhodamine (acceptor) with an effective distance of 55 Å; IAEDANS (donor) and Fluorescein (acceptor) with an effective distance of 46 Å; and Fluorescein (donor) and QSY-7 dye (acceptor) with an effective distance of 61 Å (Molecular Probes).

[0142] Quantitative assays for nucleic acid detection also can be performed according to the present invention. The amount of secondary probe bound to a microarry spot can be measured and can be related to the amount of nucleic acid target which is in the sample. Dilutions of the sample can be used along with controls containing known amount of the target nucleic acid. The precise conditions for performing these steps will be apparent to one skilled in the art.

[0143] Embodiments to Reduce Secondary Probe Background Binding

[0144] The present invention provides several embodiments useful for reducing background hybridization under indirect detection occurring when the secondary probe hybridizes to unhybridized (i.e., non-intermolecularly hybridized) hairpin probe on the solid support.

[0145] 1. Hairpin Formation of Unhybridized Hairpin Probes:

[0146] Subsequent to achieving intermolecular probe hybridization to target nucleic acid, conditions are adjusted to support intramolecular hybridization for all unhybridized hairpin probes. Detectably labeled secondary probe is then added and the binding subsequently determined.

[0147] 2. Crosslinking of Unhybridized Hairpin Probes:

[0148] Cross linking can be achieved by covalent or noncovalent strategies. Covalent intermolecular crosslinking of intramolecular hybridized probe is achieved by an agent such as psoralen. Such agent can be incorporated into the secondary probe during its preparation or can be added to the probe-target hybridization mixture following the step of intermolecular hybridization.

[0149] Noncovalent crosslinking of intramolecular hybridized probe is achieved by a ligand-receptor interaction such as avidin-biotin. For example, the probe can be synthesized with at least two biotin moieties, one in each arm of the hybridizing hairpin suitable for crosslinking by avidin or streptavidin.

[0150] In either approach, probe crosslinking is optionally preceded with the use of a hybridization step that supports intramolecular hairpin formation.

[0151] 3. Differential Destruction of Inter-Versus Intra-Molecularly Hybridized Probe

[0152] In this embodiment, the hairpin probe is prepared comprising a modified phosphodiester nucleotide DNA sequence in one strand of the double stranded portion of the probe and a complementary RNA sequence or DNA sequence in the other strand of the double stranded portion of the probe, wherein the modified phosphodiester nucleotide DNA is not recognizable by a particular DNA or RNA nuclease. Following hybridization of the target sample nucleic acid or optionally following a subsequent step of providing hybridization conditions supporting intramolecular hybridization of unhybridized probe, the nuclease is added to partially degrade the intermolecularly hybridized probe, thereby exposing an unique DNA sequence not available in the intramolecularly hybridized probe. A detectably labeled secondary probe that hybridizes with the unique exposed sequence is then used to detect original intermolecular hybridization between the target and the hairpin probe (which occurred prior to nuclease digestion of this hybrid).

[0153] For example, the hairpin probe can be prepared with methylphosphonate DNA for one intramolecularly hybridizing sequence and with RNA for the other intramolecularly hybridizing sequence. When such a probe is intermolecularly hybridized to a target nucleic acid, the RNA portion of the hairpin is sensitive to digestion with RNase H, which destroys the hybrid but which results in a single stranded methylphosphonate DNA sequence that is now available for detection by hybridization to an appropriate complementary secondary probe. The background is reduced in this format because probes that do not intermolecularly hybridize are not subject to degradation by the nuclease and do not have the unique exposed sequence to hybridize with the secondary probe.

[0154] In another example, certain enzymatic digestions, e.g., restriction enzyme digestion, can be used to selectively protect intermolecularly hybridized probe and target nucleotide sequence. After hybridization, such enzymatic cleavage sites can be created in either the probe or the intermolecular hybrid. For example, certain restriction enzymes, e.g., BstNI, do not cleave single-stranded substrate. After hybridization with the target DNA, a portion of the hybridized DNA becomes single-stranded and is resistant to the BstNI digestion, whereas the unhybridized DNA probe remains double-stranded and is sensitive to the BstNI digestion. Other variations can be made so that the hybridized probe, but not the unhybridized probe, is sensitive to the enzymatic digestion. This can be achieved by using modified nucleotides in the intramolecular probe hybrids which renders it resistant to the enzymatic digestion. After intermolecular hybridization, enzymatic cleavage sites can be created in the intermolecular hybrid (see e.g., U.S. Pat. No. 5,932,450). Such modifications include the use of methylphosphonates, phosphorothioates, peptide internucloetides and other suitable moieties and/or linkages in the hairpin probe.

[0155] Test Samples and Target Nucleotide Sequences

[0156] Target nucleotide sequences detectable using the hybridization methods disclosed herein can be DNA, RNA or any other naturally or synthetic nucleic acid sample. Test samples can include body fluids, such as urine, blood, semen, cerebrospinal fluid, pus, amniotic fluid, tears, or semisolid or fluid discharge, e.g., sputum, saliva, lung aspirate, vaginal or urethral discharge, stool or solid tissue samples, such as a biopsy or chorionic villi specimens. Test samples also include samples collected with swabs from the skin, genitalia, or throat. Test samples can be processed to isolate nucleic acid by a variety of means well known in the art (See generally, Ausubel (Ed.) Current Protocols in Molecular Biology, 2. Preparation and Analysis of DNA and 4. Preparation and Analysis of RNA, John Wiley & Sons, Inc. (2000)).

[0157] Although the present method can be used in solution, it is preferably conducted in chip format, e.g., by using the probe(s) immobilized on a solid support.

[0158] Similarly, although the present method can be used to analyze a single sample with a single probe at a time. Preferably, the method is conducted in high-throughput format. For example, a plurality of samples can be analyzed with a single probe simultaneously, or a single sample can be analyzed using a plurality of probes simultaneously. More preferably, a plurality of samples can be analyzed using a plurality of probes simultaneously.

[0159] Any suitable samples can be analyzed using the present method. Preferably, a biosample is analyzed using the present method. For example, a biosample of plant, animal, human, fungal, bacterial and viral origin can analyzed. If a sample of a mammalian or human origin is analyzed, the sample can be derived from a particular tissue or organ. Exemplary tissues include connective, epithelium, muscle or nerve tissue. Exemplary organs include eye, annulospiral organ, auditory organ, Chievitz organ, circumventricular organ, Corti organ, critical organ, enamel organ, end organ, external female gential organ, external male genital organ, floating organ, flower-spray organ of Ruffini, genital organ, Golgi tendon organ, gustatory organ, organ of hearing, internal female genital organ, internal male genital organ, intromittent organ, Jacobson organ, neurohemal organ, neurotendinous organ, olfactory organ, otolithic organ, ptotic organ, organ of Rosenmüller, sense organ, organ of smell, spiral organ, subcommissural organ, subfornical organ, supernumerary organ, tactile organ, target organ, organ of taste, organ of touch, urinary organ, vascular organ of lamina terminalis, vestibular organ, vestibulocochlear organ, vestigial organ, organ of vision, visual organ, vomeronasal organ, wandering organ, Weber organ and organ of Zuckerkandl. Preferably, samples derived from an internal mammalian organ such as brain, lung, liver, spleen, bone marrow, thymus, heart, lymph, blood, bone, cartilage, pancreas, kidney, gall bladder, stomach, intestine, testis, ovary, uterus, rectum, nervous system, gland, internal blood vessels, etc, are analyzed.

[0160] Alternatively, pathological samples in connection with various diseases or disorders or infections can be analyzed. Exemplary diseases or disorders include neoplasms (neoplasia), cancers, immune system diseases or disorders, metabolism diseases or disorder, muscle and bone diseases or disorders, nervous system diseases or disorders, signal diseases or disorders and transporter diseases or disorders. The infection to be analyzed can be fungal, bacterial and viral infection.

[0161] The present methods can be used to detect or analyze any nucleic acids from essentially any species of organism, including, for example, Acintobacter, Actinomyces, Aerococcus, Aeromonas, Alclaigenes, Bacillus, Bacteriodes, Bordetella, Branhamella, Bevibacterium, Campylobacter, Candida, Capnocytophagia, Chlamydia, Chromobacterium, Clostridium, Corynebacterium, Cryptococcus, Deinococcus, Enterococcus, Erysielothrix, Escherichia, Flavobacterium, Gemella, Gonorrhea, Haemophilus, Klebsiella, Lactobacillus, Lactococcus, Legionella, Leuconostoc, Listeria, Micrococcus, Mycobacterium, Neisseria, Nocardia, Oerskovia, Paracoccus, Pediococcus, Peptostreptococcus, Propionibacterium, Proteus, Psuedomonas, Rahnella, Rhodococcus, Rhodospirillium, Staphlococcus, Streptomyces, Streptococcus, Vibrio, and Yersinia. Also included are viruses such as the hepatitis viruses and human immunodeficiency viruses (HIV).

[0162] E. Method for Detecting a Target Nucleotide Sequence Using Immobilized Probe Arrays

[0163] In yet another aspect, the present invention provides a method for detecting a target nucleotide sequence in a sample, comprising the steps of: a) providing an array of oligonucleotide probes immobilized on a solid support suitable for use in nucleic acid hybridization having immobilized thereon a plurality of oligonucleotide probes, at least one of the probes comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with; b) contacting the array of probes provided in step a) with a sample containing or suspected of containing the target nucleotide sequence under conditions that favor intermolecular hybridization between the probes and the target nucleotide sequence over intramolecular hybridization of the probes themselves; and c) assessing the intermolecular hybrids formed in step b), whereby presence of the intermolecular hybrids indicates the presence of the target nucleotide sequence in the sample.

[0164] Preferably, at least a quarter, a half, two-thirds or each and all of the probes in the array comprise a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.

[0165] To be used in the present methods, at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequences located within said single stranded loop must collectively form a region that is complementary to a target nucleotide sequence to be detected. Preferably, the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence. Also preferably, the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence. The single stranded loop of the probe must contain more than 2 nucleotides. For example, The single stranded loop of the probe can comprise at least 3, 4, 5, 6, 7, 8, 9, 10, 15 or more nucleotides.

[0166] Hybridization conditions, means for detecting the intermolecular hybrid, the secondary probes and test samples and target nucleotide sequences described in the above Section D can also be used in connection with the methods described in this Section E.

[0167] F. Method for Transcribing and/or Amplifying a Target DNA Sequence

[0168] In yet another aspect, the present invention provides a method for transcribing and/or amplifying an oligonucleotide probe sequence, which method comprises the steps of: a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions and contains a promoter sequence, and wherein at least a portion of said nucleotide sequence located within said single stranded loop is complementary to a DNA sequence and said portion of said nucleotide sequence comprises both ribonucleotide sequence and deoxyribonucleotide sequence; b) contacting said probe provided in step a) with said DNA sequence under suitable conditions to form a probe/DNA duplex, preferably without opening said double stranded segment of said probe; c) cleaving said ribonucleotide sequence within said portion of said nucleotide sequence complementary to said DNA sequence by RNase H treatment to open said single stranded loop; and d) synthesizing a RNA sequence using a RNA polymerase that is compatible with said promoter contained within said double stranded segment of said probe, whereby at least a portion of said single stranded loop is transcribed. The RNase H cleavage step is important because if the loop structure is not opened, no appreciable level of transcription will occur under conditions that are normally suitable for transcription, e.g., in the presence of normal level of RNA polymerase and ribonucleotides with normal incubation time and temperature, etc.

[0169] Any suitable promoter and RNA polymerase can be used so long as the promoter and the RNA polymerase are compatible. For example, commonly used promoters and RNA polymerases can be used (See generally, Ausubel (Ed.) Current Protocols in Molecular Biology, 3.8. DNA-Dependent RNA polymerases, John Wiley & Sons, Inc. (2000)). In one embodiment, E. coli promoter and E. coli RNA polymerase can be used (Chamberlin, The Enzymes, Vol. 15B (P. D. Boyer, ed.) pp. 61-68, Academic Press, NY (1982)). In another embodiment, bacteriophage promoters, e.g., T7, T3 and SP6, and corresponding RNA polymerases, e.g., T7, T3 and SP6 RNA polymerases, can be used (Davanloo et al., Proc. Natl. Acad. Sci. U.S.A., 81:2035-2039 (1984); Studier and Moffatt, J. Mol. Biol., 189:113-130 (1986); Tabor and Richardson et al., Proc. Natl. Acad. Sci. U.S.A., 82:1074-1078 (1985); Morris et al., Gene, 41:193-200 (1986); Butler and Chamberlin, J. Biol. Chem., 257:5772-5778 (1982); and Krieg and Melton, Nucl. Acids Res., 12:7035-7056 (1984)). Commercially available promoters and RNA polymerases can also be used.

[0170] Other promoters, regulatory sequences, e.g., enhancers and other negative regulatory sequences, and RNA polymerases of animal, including mammalian and human, plant, fungal, bacteria and viral, including bacteriophage, origin, whether in naturally occurring form or in modified form, can also be used. For example, eukaryotic RNA polymerases, including RNA polymerases I, II and III, can be used. Promoters and corresponding RNA polymerases known in the art can also be used. Such exemplary promoters which may be used include, but are not limited to, the SV40 early promoter (Bemoist and Chambon, Nature, 290:304-310 (1981)), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., Cell, 22:787-797 (1980)), the herpes thymidine kinase promoter (Wagner et al., Proc. Natl. Acad. Sci. USA, 78:1441-1445 (1981)), the regulatory sequences of the metallothionein gene (Brinster et al., Nature, 296:39-42 (1982)); prokaryotic expression vectors such as the β-lactamase promoter (Villa-Kamaroff et al., Proc. Natl. Acad. Sci. USA, 75:3727-3731 1978)) or the tac promoter (DeBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983); see also “Useful Proteins from Recombinant Bacteria”: in Scientific American, 242:79-94 (1980)); plant expression vectors comprising the nopaline synthetase promoter (Herrar-Estrella et al., Nature, 303:209-213 (1984)) or the cauliflower mosaic virus 35S RNA promoter (Garder et al., Nucleic Acids Res., 9:2871 (1981)), and the promoter of the photosynthetic enzyme ribulose bisphosphate carboxylase (Herrera-Estrella et al., Nature, 310:115-120 (1984)); promoter elements from yeast and other fungi such as the Gal4 promoter, the alcohol dehydrogenase promoter, the phosphoglycerol kinase promoter, the alkaline phosphatase promoter, and the following animal transcriptional control regions that exhibit tissue specificity and have been utilized in transgenic animals: elastase I gene control region which is active in pancreatic acinar cells (Swift et al., Cell, 38:639-646 (1984); Ornitz et al., Cold Spring Harbor Symp. Quant. Biol., 50:399-409 (1986); and MacDonald, Hepatology 7:425-515 (1987)); insulin gene control region which is active in pancreatic beta cells (Hanahan et al., Nature, 315:115-122 (1985)), immunoglobulin gene control region which is active in lymphoid cells (Grosschedl et al., Cell, 38:647-658 (1984); Adams et al., Nature, 318:533-538 (1985); and Alexander et al., Mol. Cell Biol., 7:1436-1444 (1987)), mouse mammary tumor virus control region which is active in testicular, breast, lymphoid and mast cells (Leder et al., Cell, 45:485-495 (1986)), albumin gene control region which is active in liver (Pinckert et al., Genes and Devel., 1:268-276 (1987)), alpha-fetoprotein gene control region which is active in liver (Krumlauf et al., Mol. Cell. Biol., 5:1639-1648 (1985); and Hammer et al., Science, 235:53-58 1987)), alpha-1 antitrypsin gene control region which is active in liver (Kelsey et al., Genes and Devel., 1:161-171 (1987)), beta globin gene control region which is active in myeloid cells (Mogram et al., Nature, 315:338-340 (1985); and Kollias et al., Cell, 46:89-94 (1986)), myelin basic protein gene control region which is active in oligodendrocyte cells of the brain (Readhead et al., Cell, 48:703-712 (1987)), myosin light chain-2 gene control region which is active in skeletal muscle (Sani, Nature, 314:283-286 (1985)), and gonadotrophic releasing hormone gene control region which is active in gonadotrophs of the hypothalamus (Mason et al., Science, 234:1372-1378 (1986)).

[0171] Any suitable hairpin probes can be used. For example, hairpin probes having at least a portion of the nucleotide sequences located within the double stranded segment and a portion of the nucleotide sequence located within the single stranded loop that collectively form a region that is complementary to the target DNA sequence can be used. Other hairpin probes, including the ones described in the above Section B and those described in the co-pending U.S. patent application Ser. No. 09/616,761, filed Jul. 14, 2000, can also be used.

[0172] In one specific embodiment, the method further comprises a step of reverse transcribing the synthesized RNA sequence into a DNA sequence. Any suitable RNA-dependent DNA polymerases, i.e., reverse transcriptases, can be used. For example, avian myeloblastosis virus (AMV) or Moloney murine leukemia virus (MMLV) reverse transcriptases can be used (See generally, Ausubel (Ed.) Current Protocols in Molecular Biology, 3.7. RNA-Dependent DNA polymerases, John Wiley & Sons, Inc. (2000); Roth et al., J. Biol. Chem., 260:9326-9335 (1985); Taylor et al., Biochem. Biophys. Acta, 442:324-330 (1976); and Verma, Reverse transcriptase, The Enzymes, Vol. 14A (P. D. Boyer, ed.) pp. 87-104, Academic Press, NY (1977)). Commercially available reverse transcriptases can also be used.

[0173] In a preferred embodiment, the RNA synthesis and the reverse transcription can be conducted for a plurality of cycles to amplify the target DNA sequence.

F. EXAMPLES Example 1

[0174] Human Papilloma Virus Genotyping

[0175] Immobilization of nucleic acids and oligonucleotides are known in the art (Dattagupta et al., Analytical Biochemistry, 177:85-89 (1989); Saiki et al., Proc. Natl. Acad Sci., USA, 86:6230-6234 (1989); and Gravitt et al., J. Clin. Micro., 36:3020-3027 (1998)). Methods described in those references can be used in the present invention. human papilloma virus (HPV) probe sequences as described in Gravitt et al., (supra) are synthesized in a commercially available oligonucleotide synthesizer. During the synthesis, following changes are made:

[0176] i) The probes are extended at the 3′ end up to 30 extra nucleotide residues. First 9 residues are made of dT to function as spacer for the hairpin structure.

[0177] ii) The rest (21 residues) is complementary to the probe sequence and sequentially organized as 7 deoxy-6 ribo-8 deoxy residues.

[0178] iii) The probe sequence has methylphosphonates complementary to the ribose residues in the chain. This will prevent RNase H digestion of the unhybridized hairpin probe. This will also reduce the Tm of the probe compared to an RNA-DNA hybrid formed with a target.

[0179] For example, the probe 5′-CAT CCG TAA CTA CAT CTT CCA-3′ (SEQ ID NO:1) is present in an oligonucleotide of the following structure: 5′-CAT-CCG-TAa-cta-caT-CTT-CCA- TTT-TTT-TTT-TGG-AAG A TG-TAG-T TA-CGG-ATG-3′ (SEQ ID NO:2) (underlined nucleotides are ribonucleotides, lower case nucleotides are methylphosphonates residues). Such an oligonucleotide is immobilized onto a membrane by BSA conjugation method and genomic HPV DNA is purified from samples by proteinase K digestion and ethanol precipitation as described in Gravitt et al (supra). The immobilized hairpin probe containing strip is hybridized with the sample DNA at 53° C. overnight in a buffer containing 0.72 M NaCl, 40 mM NaH₂PO₄ and 4 mM EDTA (pH 7.7). After hybridization, the strip is washed twice with the hybridization buffer at 57° C. and RNase H buffer once. The strip containing the hybrid is then treated with RNase H to digest the part of the hybridized probe with RNA-DNA hybrid structure. This is carried out by using 1 unit of RNase H from Sigma Chemical Co. (St. Louis, Mo.) per ml of the digestion buffer. The RNase H digestion buffer contains 20 mM tris-HCl (pH 7.5), 100 mM KCl, 10 mM MgCl₂, 0.1 mM EDTA, 0.1 mM DTT and 0.05 mg BSA per ml. By immersing the strip containing the hybrid in the digestion buffer containing the enzyme for 1 hour at 37° C., hybrids containing RNA-DNA structure is digested and under these conditions hairpin intra-molecular hybrid is not disturbed.

[0180] After the enzyme digestion, the strip is washed with hybridization buffer and a second hybridization is carried out with biotin labeled probes. The labeled probes are equal weight by weight mixtures of oligonucleotides complementary to the immobilized probe portions which become single stranded after hybridization and digestion. After the second hybridization and washing, biotin in the hybrid is detected by using a streptavidin-horseradish peroxidase conjugate chemiluminescence. This is carried out by soaking the array in a solution containing 1:1 mixture of 0.5 mM Luminol and hydrogen peroxide and wrapping the whole contents with a plastic wrap, e.g., “SARAN WRAP”. The light emission is recorded on a “POLAROID” film. Biotin sites appear as white spots on the film.

[0181] The sites where biotin is detected is the site of hybridization of the target sample and the corresponding sequence is the sequence of the target present in the sample.

Example 2

[0182] Assay for Mycobacterium TB Drug Resistance by Post Hybridization Blocking of Immobilized Probes

[0183] Using the sequence information disclosed in Telenti et al., Lancet, 341:647-650 (1993), Beenhouwer et al., Tubercule and Lung Disease, 76:425-430 (1995) designed PCR primers and probes for detection of mutated sequence in a rifampicin resistance of mycobacterium tuberculosis organism. The present method uses identical primers for PCR and immobilized probe sequences. The probe sequences are extended as described in example 1 to have a hairpin structure which is immobilized and at nucleotide position 45 a psoralen moiety is covalently attached. Primer sequences for amplification are: 5′GAG AAT TCG GTC GGC GAG CTG ATCC3′ (SEQ ID NO:3) and 5′CGA AGC TTG ACC CGC GCG TAC ACC3′. (SEQ ID NO:4)

[0184] These primers produce a 395 bp amplicon after PCR. PCR is done in a buffer containing 50 mM KCl, 10 mM tris-HCl (pH 8.3), 2.2 mM MgCl₂, 200 mM each of four dNTPs, 0.01% gelatin and 1 U of Taq Polymerase. Typical amplification is done for 40 cycles (94° C., 58° C. and 72° C. at 45 sec.) For the synthesis of labeled amplicons as detection probe, PCR is done by using a mixture of dNTPs containing biotinylated dUTP and TTP in a 1:10 mixture and others in the same concentrations as above.

[0185] A typical 48-mer long hairpin probe has the following structure after immobilization:

[0186] 5′**CAA TTC ATG GAC CAG AAC AAC CCG TTT TTT TTT CGG GTT GTT CTG CTC CAT GAA TTG 3′ (SEQ ID NO:5). The sequence underlined is synthesized in an oligonucleotide synthesizer. In between nucleotides TT a psoralen modification is used to crosslink unhybridized hairpin probe after hybridization with the sample. First, the oligonucleotide with an amino terminated linker in the TT position is synthesized in a synthesizer. Such linkers have been described in U.S. Pat. No. 5,541,313. The amino terminated linker containing oligonucleotide is then reacted with an N-hydroxysuccinimide (NHS) activated 4′-carboxtrioxsalen derivative in dirnethyl sulfoxide. Such a compound is synthesized by reacting 4′-aminomethyl trioxsalen (Sigma Chemical Co. St. Louis, Mo.) with succinic anhybride. The resulting carboxy compound is then further activated to produce NHS-ester which is used for the reaction. After the reaction the oligonucleotide is purified on a reverse phase HPLC column. The oligonucleotide is then phosphorylated at the 5′-end by conventional method using polynucleotide kinase. The solid support containing immobilized oligonucleotide of structure 5′-TTT TTT TTT CAA TTC ATG-3′ (SEQ ID NO:6) is hybridized with 5′-phosphorylated GAC CAG AAC AAC CCG TTT TTT TTT CGG GTT GTT CTG CTC CAT GAA TTG-3′ (SEQ ID NO:7). The hybrid is ligated by using a T4 DNA ligase. This produces an immobilized probe with a photocrosslinking moiety.

[0187] A set of immobilized probes on polystyrene beads with sequences of all different modifications representative of the mutations responsible for rifampicin resistance is prepared as describe above. Each immobilized probe is dispensed in a microtitre plate well. Five microliters of the amplicons are aliquoted into each well followed by 40 microliters of hybridization buffer of example 1. Hybridization is done at 56° C. for 60 minutes. After hybridization the beads are washed as described in example 1. The microtiter plate is exposed to 312 nm light for 60 minutes using a transilluminator at 25° C. This process crosslinks all unhybridized immobilized probes and hybrid(s) to the solid support. The hybrids are detected by a second hybridization with a labeled probe as the PCR amplicon containing biotin as described above. Biotin in the hybrid is detected by a streptavidin-horseradish peroxidase enzyme system.

Example 3

[0188] Post Hybridization Labeling of Hybrids

[0189] Example 2 is repeated without the use of biotinylated labeled amplicon. After hybridization, washing and irradiation, the hybrids are labeled for detection by hybridization with a aminomethyl trioxsalen and enzyme labeled degenerate pentamer oligonucleotides. The double labeled oligonucleotides are synthesized as follows:

[0190] First, a psoralen labeled ribonucleotide is synthesized as described in Dattagupta et al., U.S. Pat. No. 5,587,472. Commercially available aminomethyltrioxsalen from Sigma Chemical Co. is derivatized with a dibasic acid anhydride like succinic anhydride. The resulting acid is mixed with (1:3:3 molar ratio) 1-(3-dimethylaminopropyl)-3-ethylcarbodimide methiodide and N-hydroxysulfosuccinimide (sodium salt) in DMF and heated to 50° C. for 7.5 hours. According to TLC (toluene/ethanol .5:4, silicagel), most of the carboxylic acid has been converted to the N-hydroxysulfosuccininimide ester. The reaction mixture is cooled to room temperature and a solution of 8-(6-aminohexyl) mninoadenosine-5′-triphosphate (Li-salt, Sigma, 10⁻⁵ mol) in 100 μl water and 20 μl pyridine (2.5×10⁻⁴ mol) is added. After stirring at room temperature overnight, only traces of a new compound are detectable. The mixture is then sonicated for 3 hours, 2 mg of 4-dimethylaminopyridine (1.6×10⁻⁵) is added and the mixture is sonicated for an additional 5 hours. According to TLC (t-BuOH 3.5/acetone 2.5/conc. ammonia 1.5/HOAc 1.5/water, cellulose), a new product is now easily detectable. The reaction mixture is evaporated to dryness under vacuum. Chromatography of the residue (3 times) on a Sephadex G 10 column (Pharmacia) with water as eluent gives aminomethyltrioxsalen labeled ATP (ps-ATP).

[0191] The psoralen labeled ribonucleotide (ps-ATP described above) is incorporated into degenerate tetramer oligonucleotides by terminal deoxynucleotidyl transferase (Pharmacia) as follows:

[0192] 1.8 μg oligonucleotide (synthesized in an Applied Biosystems Inc.'s (Foster City, Calif.) automated oligonucleotide synthesizer using their reagents) and 2.5 μg ps-ATP are dissolved in a reaction buffer containing 140 mmol/l K-cacodylate, 30 mmol/l Tris-buffer (pH 7.6), 1 mmol/l cobalt chloride and 0.1 mmol/l dithiothreitol (DTT) (total volume 50 μl). Enzymatic elongation is achieved by addition of 22 U terminal deoxynucleotidyl transferase and incubation for 16.5 hours at 37° C.

[0193] 20% denaturing polyacrylamide gel electrophoresis shows a DNA band under UV shadowing which can be detected visually.

[0194] ps-ATP labeled oligonucleotide is further treated if necessary, with sodium hydroxide to digest all but the last ribonucleotide residue which contains one aminomethyl trioxsalen moiety.

[0195] Similar method can be used to synthesize oligonucleotide with any ribonucleotide (A,U,G, C riboT or any other ribonucleoside or deoxyribonucleoside) at its 3′ end.

[0196] All different degenerate sequences are made in a synthesizer. At the 3′-end of the pentamer, a psoralen moiety as described above and at the 5′-end an enzyme like horseradish peroxidase is covalently attached following the method described in U.S. Pat. No. 5,541,313. Such synthetic molecules are available commercially from Gemini Biotech Ltd. The Woodlands, Tex. These degenerate sequences hybridize to any complementary hybridizable sequence at 30° C. After hybridization and a second irradiation, the labeled petamers are covalently linked to the hybrid or single stranded hybridized probes. Unreacted pentamers are washed at 37° C. and hybrids are detected by the enzyme assay as described above.

Example 4 The Minimum Number of Ribonucleotides in DNA/RNA Chimeric Oligonucleotide for RNase H Cleavage

[0197] RNase H hydrolyzes RNA strand in an RNA-DNA duplex. RNase H can also hydrolyze a short ribonucleotide stretch in a DNA-RNA-DNA fragment, when such DNA-RNA-DNA fragment binds with a complementary DNA strand. In order to determine the minimum number of ribonucleotides to be cleaved by RNase H in the DNA-RNA-DNA fragment, four kinds of oligonucleotides with different number of ribonucleotides (bold and underlined) were designed, AGT02008: TTTTTTTAAAATTTTTTTTT (SEQ ID NO:8), AGT02012: TTTTTTTAAAATTTTTTTTT (SEQ ID NO:9), AGT02013: TTTTTTTAAAATTTTTTTTT (SEQ ID NO:10) and AGT02014: TTTTTTTAAAATTTTTTTTT (SEQ ID NO:11). These oligos were mixed with a complement DNA oligo AGT02009: AAAAAAATTTTAAAAAAAAA (SEQ ID NO: 12) at 37° C. for 25 minutes. Five units of RNase H were added and incubated at 37° C. for 30 minutes. FIG. 3A shows that RNase H can cleave four (4) ribonucleotides in the DNA/RNA chimeric oligo (comparing lane 2 with lanes 4, 6, and 8 of FIG. 3A.). With high concentration, e.g., about 50 units/μl, three (3) ribonucleotides can also be cut by RNase H (see lane 6 of FIG. 3B.). Two (2) ribonucleotides in the DNA/RNA chimeric oligo cannot be cut by RNase H under any condition. Therefore, four (4) ribonucleotides are the minimum numbers for RNase H cleavage with normal RNase H concentration, e.g., about 5 units/μl.

Example 5

[0198] Mismatch Inhibits RNase H Activity

[0199] A hairpin DNA probe contains a loop region and a stem region. When the target DNA (complement DNA) binds with the hairpin DNA probe, they can open the hairpin structure in the hairpin probe to form a duplex structure. If the target DNA doesn't complement to at least a portion of the sequence of the hairpin DNA probe, the hairpin DNA probe maintains its hairpin structure. If a RNase H cleavage site is present in the stem region, some modifications in hairpin DNA probe are need to inhibit the RNase H cleavage. When the hairpin probe binds with the target DNA, the duplex formed between the hairpin probe containing the RNase H cleavage site and the target DNA strand can be cleaved by RNase H. If the target DNA does not bind to the hairpin probe, the hairpin probe maintains original hairpin structure and cannot be cleaved by RNase H. Accordingly, the binding and non-binding between the hairpin probe and the target DNA strand can be determined by assessing RNase H cleavage. In order to find a condition that ablates RNase H cleavage, oligos AGT02020: AAAAAAAGTTTAAAAAAAAA (SEQ ID NO:13), AGT02021: AAAAAAATGTTAAAAAAAAA (SEQ ID NO:14), AGT02022: AAAAAAAGGTTAAAAAAAAA (SEQ ID NO:15) and AGT02023: AAAAAAAGTGTAAAAAAAAA (SEQ ID NO:16) containing mismatch(es) to the target DNA sequence were tested in the hybridization/RNase H cleavage assay. The oligos were mixed with the target DNA oligo AGT02009 (SEQ ID NO:12) at 37° C. for 25 minutes. One (1) unit of RNase H was added and incubated at 37° C. for 30 minutes. FIG. 4A. shows that two mismatch sites in the duplex ablated RNase H cleavage (Lanes 12 and 15 of FIG. 4A.). The effect of one mismatch site is less than two mismatch sites and it has polarity effect. The mutation site at position 2 has stronger inhibition effect than mutation site at position 3 (Comparing lanes 6 and 9 of FIG. 4A.). It was also found that there is no sequence preference at position 2 to inhibit RNase H cleavage because the tests using oligos AGT02021 (SEQ ID NO:14), AGT02024: AAAAAAATCTTAAAAAAAAA (SEQ ID NO:17) and AGT02025: AAAAAAATATTAAAAAAAAA (SEQ ID NO:18) containing different mismatches at the same position gave similar blocking effect (See FIG. 4B).

Example 6

[0200] RNase H Can Be Used in Hairpin Structure Cleavage Assay

[0201] Linear probes were used in the experiments described in Examples 4 and 5. In this experiment, two hairpin DNA probes containing 4 ribonucleotides in 5′ and 3′ double stranded region (relative to the position of the single stranded loop region), AGT2010: GCACATTCTCAUCUCTGAAAACTTCCGTGGTTTCAGAGAUGAGAATGT GC (SEQ ID NO:19) (the loop region is italicized) and AGT02011: GCACATTCTCATCTCTGAAAACTTCCGTGGTTTCAGAGAUGAGAATGTG C (SEQ ID NO:20) (the loop region is italicized) were used. The hairpin probes, alone or mixed with their complement target DNA AGT2028: CGTGTAAGAGTTAAGACTTTTGAAGGCACC (SEQ ID NO:21) and AGT02029: AAGGCACCAAAGTCTAGACTCTTACACG (SEQ ID NO:22), respectively, were heated to 94° C. for 2 minutes. The temperature was then lowered to different annealing temperatures for 15 minutes. One (1) unit of RNase H was added and incubated at 37° C. for 30 minutes. Lane 2 of FIGS. 5A. and 5B. show that both hairpin DNA probes were cleaved by RNase H and there is no difference whether the RNase H cleavage site is located in 5′ or 3′ end of the single stranded loop region. In contrast, the two mismatch sites within the target DNA ablated the RNase H cleavage (Lanes 3 to 7 of FIGS. 5A and 5B.). Surprisingly, different annealing temperatures do not affect duplex formation and/or RNase H cleavage inhibition.

Example 7

[0202] The Hairpin Probe Can Bind With Single Strand Target Oligo at a Wide Range of Temperatures

[0203] The hairpin DNA probe AGT02011 (SEQ ID NO:20) was heated to 94° C. for 2 minutes, and annealed at 60° C. for 10 minutes to form the hairpin structure. AGT02011 was also mixed with the target single strand DNA AGT02028 (SEQ ID NO:21) at different annealing temperatures for 25 minutes. FIGS. 6A. and 6B. show that there is no difference in duplex formation between the hairpin probe and the target DNA at a wide range of annealing temperatures from 18° C. to 85° C. It indicates that the hairpin structure and duplex formation is essentially independent of annealing temperatures. Additional experiments were conducted to assess this effect of annealing time. Hairpin probe was mixed with the target DNA at room temperature for 1 to 5 minutes and then loaded into the gel. The result shows that the duplex was formed with annealing time as short as 1 minute (FIG. 6C, lane 3). Even when annealing was conducted at 4° C., the hairpin probe still bound with the target DNA to form a duplex (FIG. 6C lane 8).

Example 8

[0204] The Sequence Specificity of Hairpin Probe

[0205] Specificity is a very important factor for hybridization assay. The hairpin probe used in this experiment is AGT02011 (SEQ ID NO:20). Different target DNAs containing mismatches with AGT02011 in its loop region, stem region and the junction between the loop and the stem regions were tested on their effect on binding. AGT02029 (SEQ ID NO:22) has two mismatch sites in the stem region of AGT02011. AGT02039: TGAAGGCACCAAACGTGAACTATCAACTAC (SEQ ID NO:23) is 100% match at loop region and 25% match in stem region of AGT02011. AGT02040: TCATGCCTCGAAAGTCTACTCTCTTACACG (SEQ ID NO:24) is 50% match in loop region and 100% match in stem region of AGT02011. AGT02048: TGAAGGCTAGAAAGTCTAGACTCTTACACG (SEQ ID NO:25) has 3 mismatch sites in the junction of loop and stem regions of AGT02011. FIG. 7. shows that only AGT02029 can bind with AGT02011 to form the duplex form. The effect of mutation in the loop region seem to be more serious than mutation in the stem region (Comparing lanes 3 and 7 of FIG. 7.).

Example 9

[0206] The Loop Region of a Hairpin Probe Play an Important Role in Target Sequence Binding

[0207] Three target DNAs with different length complementary to the loop region of the hairpin probe AGT02011 (SEQ ID NO:20) were used in this experiment. AGT02029 (SEQ ID NO:22), AGT02035: TGAAGGCACCAAAGTCTAGACTCTTACACG (SEQ ID NO:26) and AGT02036: CCAAAGTCTAGACTCTTACACG (SEQ ID NO:27) have 8, 10 and 2 oligonucleotides that are complementary to the loop region of the hairpin probe AGT02011, respectively. FIG. 8. shows that AGT02036 can't bind to AGT02011 to form a duplex (See FIG. 8, lane 7). This result indicates that binding between the loop region of the hairpin probe with target DNA may help the hairpin to open at low temperature, e.g., about 4° C. Complementary of two nucleotides in the loop region to target DNA can't give enough energy to open the hairpin structure at low temperature.

[0208] The above examples are included for illustrative purposes only and is not intended to limit the scope of the invention. Since modifications will be apparent to those of skill in this art, it is intended that this invention be limited only by the scope of the appended claims.

1 27 1 21 DNA Artificial Sequence Oligonucleotide 1 catccgtaac tacatcttcc a 21 2 51 DNA Artificial Sequence Oligonucleotide 2 catccgtaac tacatcttcc attttttttt tggaagatgt agttacggat g 51 3 25 DNA Artificial Sequence Primer 3 gagaattcgg tcggcgagct gatcc 25 4 24 DNA Artificial Sequence Primer 4 cgaagcttga cccgcgcgta cacc 24 5 57 DNA Artificial Sequence Long hairpin probe 5 caattcatgg accagaacaa cccgtttttt tttcgggttg ttctgctcca tgaattg 57 6 18 DNA Artificial Sequence Immobilized oligonucleotide 6 tttttttttc aattcatg 18 7 48 DNA Artificial Sequence Phosphorylated oligonucleotide 7 gaccagaaca acccgttttt ttttcgggtt gttctgctcc atgaattg 48 8 20 DNA Artificial Sequence Oligonucleotide AGT02008 8 tttttttaaa attttttttt 20 9 20 DNA Artificial Sequence Oligonucleotide AGT02012 9 tttttttaaa attttttttt 20 10 20 DNA Artificial Sequence Oligonucleotide AGT02013 10 tttttttaaa attttttttt 20 11 20 DNA Artificial Sequence Oligonucleotide AGT02014 11 tttttttaaa attttttttt 20 12 20 DNA Artificial Sequence Complement DNA oligo AGT02009 12 aaaaaaaaat tttaaaaaaa 20 13 20 DNA Artificial Sequence Oligo AGT02020 13 aaaaaaaaat ttgaaaaaaa 20 14 20 DNA Artificial Sequence Oligo AGT02021 14 aaaaaaaaat tgtaaaaaaa 20 15 20 DNA Artificial Sequence Oligo AGT02022 15 aaaaaaaaat tggaaaaaaa 20 16 20 DNA Artificial Sequence Oligo AGT02023 16 aaaaaaaaat gtgaaaaaaa 20 17 20 DNA Artificial Sequence Oligo AGT02024 17 aaaaaaaaat tctaaaaaaa 20 18 20 DNA Artificial Sequence Oligo AGT02025 18 aaaaaaaaat tataaaaaaa 20 19 50 DNA Artificial Sequence DNA/RNA hybrid (1) ... (50) Oligo AGT02010 19 gcacattctc aucuctgaaa acttccgtgg tttcagagat gagaatgtgc 50 20 50 DNA Artificial Sequence DNA/RNA hybrid (1) ... (50) Oligo AGT02011 20 gcacattctc atctctgaaa acttccgtgg tttcagagau gagaatgtgc 50 21 30 DNA Artificial Sequence Oligo AGT02028 21 ccacggaagt tttcagaatt gagaatgtgc 30 22 28 DNA Artificial Sequence Oligo AGT02029 22 gcacattctc agatctgaaa ccacggaa 28 23 30 DNA Artificial Sequence Oligo AGT02039 23 catcaactat caagtgcaaa ccacggaagt 30 24 29 DNA Artificial Sequence Oligo AGT02040 24 gcacattctc tcatctgaag ctccgtact 29 25 30 DNA Artificial Sequence Oligo AGT02048 25 gcacattctc agatctgaaa gatcggaagt 30 26 30 DNA Artificial Sequence Oligo AGT02035 26 gcacattctc agatctgaaa ccacggaagt 30 27 22 DNA Artificial Sequence Oligo AGT02036 27 gcacattctc agatctgaaa cc 22 

What is claimed is:
 1. An oligonucleotide probe for hybridization analysis, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.
 2. The probe of claim 1, which comprises DNA, RNA, PNA or a derivative thereof.
 3. The probe of claim 1, which comprises both DNA and RNA or derivatives thereof.
 4. The probe of claim 1, wherein the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence.
 5. The probe of claim 4, wherein the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence.
 6. The probe of claim 1, wherein the single stranded loop of the probe comprises at least 3, 4, 5, 6, 7, 8, 9, 10 or 15 nucleotides.
 7. The probe of claim 1, wherein the double stranded segment of the hairpin structure is formed between two perfectly matched nucleotide sequences or two substantially matched nucleotide sequences.
 8. The probe of claim 1, further comprising an element or a modification that facilitates intramolecular crosslinking of the probe upon suitable treatment.
 9. The probe of claim 8, wherein the element is a chemically or photoactively activatable crosslinking agent.
 10. The probe of claim 9, wherein the photoactively activatable crosslinking agent is a furocoumarin.
 11. The probe of claim 8, wherein the element is a macromolecule having multiple ligand binding sites.
 12. The probe of claim 11, wherein the macromolecule is a component of biotin-avidin binding system.
 13. The probe of claim 1, further comprising an element or a modification that renders the probe sensitive or resistant to nuclease digestion.
 14. The probe of claim 13, wherein the element is a restriction enzyme cleavage site.
 15. The probe of claim 13, wherein at least a portion of the double stranded segment of the probe is a duplex between a DNA strand and a RNA strand, the DNA strand containing methylphosphonates, and wherein at least a portion of the RNA strand is complementary to the target nucleotide sequence.
 16. An array of oligonucleotide probes immobilized on a solid support for hybridization analysis, which array comprises a solid support suitable for use in nucleic acid hybridization having immobilized thereon a plurality of oligonucleotide probes, at least one of the probes comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with.
 17. The array of claim 16, wherein the plurality of probes comprise DNA, RNA, PNA or a derivative thereof.
 18. The array of claim 16, wherein at least one of the probes comprises both DNA and RNA or derivatives thereof.
 19. The array of claim 16, wherein the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop of at least one of the probes is substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence.
 20. The array of claim 19, wherein the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop of at least one of the probes is a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence.
 21. The array of claim 16, wherein the single stranded loop of at least one of the probes comprises at least 3, 4, 5, 6, 7, 8, 9, 10 or 15 nucleotides.
 22. The array of claim 16, wherein the double stranded segment of the hairpin structure of at least one of the probes is formed between two perfectly matched nucleotide sequences or two substantially matched nucleotide sequences.
 23. The array of claim 16, wherein at least one of the probes further comprises an element or modification that facilitates intramolecular crosslinking of the probes upon suitable treatment.
 24. The array of claim 23, wherein the element is a chemically or photoactively activatable crosslinking agent.
 25. The array of claim 24, wherein the photoactively activatable crosslinking agent is a furocoumarin.
 26. The array of claim 23, wherein the element is a macromolecule having multiple ligand binding sites.
 27. The array of claim 26, wherein the macromolecule is a component of biotin-avidin binding system.
 28. The array of claim 16, wherein at least one of the probes further comprises an element or modification that renders the probe sensitive or resistant to nuclease digestion.
 29. The array of claim 28, wherein the element is a restriction enzyme cleavage site.
 30. The array of claim 28, wherein at least a portion of the double stranded segment of at least one of the probes is a duplex between a DNA strand and a RNA strand, said DNA strand contains methylphosphonates and at least a portion of said RNA strand is complementary to a target nucleotide sequence to be detected.
 31. The array of claim 16, wherein each of the oligonucleotide probe is capable of forming a target nucleotide sequence/oligonucleotide probe duplex with a different target nucleotide sequence.
 32. A method for detecting a target nucleotide sequence in a sample, which method comprises the steps of: a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be detected; b) contacting the probe provided in step a) with a sample containing or suspected of containing the target nucleotide sequence under conditions that favor intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself; and c) assessing the intermolecular hybrid formed in step b).
 33. The method of claim 32, wherein the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is substantially complementary to its corresponding nucleotide sequence in the target nucleotide sequence.
 34. The method of claim 32, wherein the portion of the nucleotide sequences located within the double stranded segment and the single stranded loop is a perfect match to its corresponding nucleotide sequence in the target nucleotide sequence.
 35. The method of claim 32, wherein the single stranded loop of the probe comprises at least 3, 4, 5, 6, 7, 8, 9 or 10,15 nucleotides.
 36. The method of claim 32, wherein the conditions that favor intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself is achieved by controlling compositions of the probe and the target nucleotide sequence so that the Tm of the intermolecular hybrid is higher than the Tm of the intramolecular hybrid.
 37. The method of claim 36, wherein the Tm of the intermolecular hybrid is at least 2° C. higher than the Tm of the intramolecular hybrid.
 38. The method of claim 36, wherein the intermolecular hybrid is a RNA:DNA, RNA:RNA or a DNA:DNA hybrid or a derivative thereof and the intramolecular hybrid is a RNA:DNA, RNA:RNA or a DNA:DNA hybrid or a derivative thereof.
 39. The method of claim 36, wherein the intermolecular hybrid is a RNA:DNA hybrid whereas the intramolecular hybrid is a DNA:DNA hybrid.
 40. The method of claim 32, wherein the target nucleotide sequence is detectably labeled and the formation of the intermolecular hybrid is assessed by detecting the label of the target nucleotide sequence in the intermolecular hybrid.
 41. The method of claim 40, wherein the label is selected from the group consisting of a chemical, an enzymatic, a radioactive, a fluorescent, a luminescent and a FRET label.
 42. The method of claim 32, wherein the formation of the intermolecular hybrid is assessed by addition of a detectably labeled secondary probe that specifically hybridizes with at least a portion of the intermolecular hybrid and the detection of a secondary intermolecular hybrid formed between the secondary probe and the original intermolecular hybrid indicates the presence of the target nucleotide sequence in the sample.
 43. The method of claim 42, further comprising a step of crosslinking the intermolecular hybrid and the intramolecular hybrid after the formation of the intermolecular hybrid but before the addition of the detectably labeled secondary probe.
 44. The method of claim 43, wherein the crosslinking step is effected via addition of a crosslinking agent subsequent to hybridization of the original probe with the target nucleotide sequence.
 45. The method of claim 43, wherein the original hairpin probe is synthesized with the crosslinking agent attached and crosslinking is achieved by addition of an appropriate agent or treatment.
 46. The method of claim 42, wherein the secondary probe specifically hybridizes with a portion of the target nucleotide sequence that is not involved in the hybridization of the target nucleotide sequence and the original probe.
 47. The method of claim 42, wherein the secondary probe specifically hybridizes with a portion of the target nucleotide sequence that is involved in the hybridization of the target nucleotide sequence and the original probe and the nucleotide sequence in the original probe that is complementary to the same portion of the target nucleotide sequence is removed prior to or concurrently with the addition of the secondary probe.
 48. The method of claim 47, wherein the hairpin structure in the original probe is formed between a DNA strand that contains methylphosphonates and a RNA strand that is complementary to the target nucleotide sequence and wherein the RNA strand, after forming a hybrid with the target nucleotide sequence but before the addition of the secondary probe, is removed by a RNase H treatment.
 49. The method of claim 42, wherein the secondary probe specifically hybridizes with a portion of the original probe that is involved in the formation of the intramolecular hybrid but is not involved in the formation of the intermolecular hybrid with the target nucleotide sequence and wherein the same portion of the original probe that remains within the unhybridized original probe is removed prior to or concurrently with the addition of the secondary probe.
 50. The method of claim 49, wherein the portion of the original probe that remains within the unhybridized original probe contains a restriction enzyme cleavage site and is removed by cleavage with said restriction enzyme.
 51. The method of claim 42, wherein the detectably labeled secondary probe is a specific probe.
 52. The method of claim 42, wherein the detectably labeled probe is a degenerate probe.
 53. The method of claim 32, wherein the probe is immobilized on a solid support.
 54. The method of claim 32, wherein a plurality of the probes immobilized on a solid support is used.
 55. The method of claim 32, wherein the sample is a biosample.
 56. The method of claim 32, wherein a plurality of samples is assayed simultaneously.
 57. The method of claim 32, wherein the oligonucleotide probe and the target nucleotide sequence is contacted at a temperature from about 4° C. to about 90° C.
 58. The method of claim 32, wherein the oligonucleotide probe and the target nucleotide sequence is contacted for a time from about 1 minute to about 60 minutes.
 59. A method for transcribing and/or amplifying an oligonucleotide probe sequence, which method comprises the steps of: a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions and contains a promoter sequence, and wherein at least a portion of said nucleotide sequence located within said single stranded loop is complementary to a DNA sequence and said portion of said nucleotide sequence comprises both ribonucleotide sequence and deoxyribonucleotide sequence; b) contacting said probe provided in step a) with said DNA sequence under suitable conditions to form a probe/DNA duplex; c) cleaving said ribonucleotide sequence within said portion of said nucleotide sequence complementary to said DNA sequence by RNase H treatment to open said single stranded loop; and d) synthesizing a RNA sequence using a RNA polymerase that is compatible with said promoter contained within said double stranded segment of said probe, whereby at least a portion of said single stranded loop is transcribed.
 60. The method of claim 59, wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to the DNA sequence.
 61. The method of claim 59, further comprising a step of reverse transcribing the synthesized RNA sequence into a DNA sequence.
 62. The method of claim 61, wherein the RNA synthesis and the reverse transcription are conducted for a plurality of cycles to amplify the probe sequence. 